wgEncodeBroadHmm Broad ChromHMM GSE38163 Chromatin State Segmentation by HMM from ENCODE/Broad Regulation  Note: these data have been converted via liftOver from the Mar. 2006 (NCBI36/hg18) version of the track. Description This track displays a chromatin state segmentation for each of nine human cell types. A common set of states across the cell types were learned by computationally integrating ChIP-seq data for nine factors plus input CTCF, H3K4me1, H3K4me2, H3K4me3, H3K27ac, H3K9ac, H3K36me3, H4K20me1, H3K27me3, and Input Control --> using a Hidden Markov Model (HMM). In total, fifteen states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements. GM12878 - lymphoblastoid cells H1-ESC - embryonic stem cells HepG2 - hepatocellular carcinoma HUVEC - Human Umbilical Vein Endothelial Cell HMEC - Human Mammary Epithelial Cells HSMM - Normal Human Skeletal Muscle Myoblasts K562 - erythroleukemia cells NHEK - Normal Human Epidermal Keratinocytes NHLF - Normal Human Lung Fibroblasts --> Display Conventions and Configuration This track is a composite track that contains multiple subtracks. Each subtrack represents data for a different cell type and displays individually on the browser. Instructions for configuring tracks with multiple subtracks are here. The fifteen states of the HMM, their associated segment color, and the candidate annotations are as follows: State 1 -  Bright Red  - Active Promoter State 2 -  Light Red  -Weak Promoter State 3 -  Purple  - Inactive/poised Promoter State 4 -  Orange  - Strong enhancer State 5 -  Orange  - Strong enhancer State 6 -  Yellow  - Weak/poised enhancer State 7 -  Yellow  - Weak/poised enhancer State 8 -  Blue  - Insulator State 9 -  Dark Green  - Transcriptional transition State 10 -  Dark Green  - Transcriptional elongation State 11 -  Light Green  - Weak transcribed State 12 -  Gray  - Polycomb-repressed State 13 -  Light Gray  - Heterochromatin; low signal State 14 -  Light Gray  - Repetitive/Copy Number Variation State 15 -  Light Gray  - Repetitive/Copy Number Variation Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods ChIP-seq data from the Broad Histone track was used to generate this track. Data for nine factors plus input and nine cell types was binarized separately at a 200 base pair resolution based on a Poisson background model. The chromatin states were learned from this binarized data using a multivariate Hidden Markov Model (HMM) that explicitly models the combinatorial patterns of observed modifications (Ernst and Kellis, 2010). To learn a common set of states across the nine cell types, first the genomes were concatenated across the cell types. For each of the nine cell types, each 200 base pair interval was then assigned to its most likely state under the model. Detailed information about the model parameters and state enrichments can be found in (Ernst et al, accepted). Release Notes This is release 1 (Jun 2011) of this track. It was lifted over from the NCBI36/hg18 version of the track, and is therefore based on the NCBI36/hg18 release of the Broad Histone track. It is anticipated that the HMM methods will be run on the newer datasets in the GRCh37/hg19 version of the Broad Histone track, and, once that happens, the new data will replace this liftOver. Credits The ChIP-seq data were generated at the Broad Institute and in the Bradley E. Bernstein lab at the Massachusetts General Hospital/Harvard Medical School, and the chromatin state segmentation was produced in Manolis Kellis's Computational Biology group at the Massachusetts Institute of Technology. Contact: Jason Ernst. Data generation and analysis was supported by funds from the NHGRI (ENCODE), the Burroughs Wellcome Fund, Howard Hughes Medical Institute, NSF, Sloan Foundation, Massachusetts General Hospital and the Broad Institute. References Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010 Aug;28(8):817-25. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. There is no restriction on the use of segmentation data. 
wgEncodeHistoneSuper ENC Histone ENCODE Histone Modification Regulation Description These tracks display maps of chromatin state of ENCODE cell types. Histones are a group of closely-related proteins that together form the nucleosome. There are six histone families: H1, H2A, H2B, H3, H4, and H5. Each nucleosome core is formed by two H2A-H2B dimers and a H3-H4 tetramer, while H1 and H5 bind the nucleosome and DNA. When histone proteins undergo post-transcriptional modifications at specific amino acids (methylation, acyetylation), these modifications (referred to as marks) perform a role in regulating the winding of the DNA around the nucleosome. This in turn regulates gene expression by controlling the accessibility of the chromatin. Histone marks vary in their effect. Promoters, enhancers, transcribed regions, and silenced regions are each associated with specific histone marks. The ChIP-seq method enables identifying regions of DNA that interact with specific histone marks. This method involves cross-linking histones and other DNA associated proteins to genomic DNA within cells using formaldehyde. The cross-linked chromatin is subsequently extracted, mechanically sheared, and immunoprecipitated using specific antibodies. This has the effect of capturing segments of DNA that are bound to the protein selected by the antibody. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments. If the antibody is specific to a given histone mark, then this procedure identifies segments of the genome associated with that mark. Display Conventions These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Geiman TM, Robertson KD. Chromatin remodeling, histone modifications, and DNA methylation-how does it all fit together? J Cell Biochem. 2002;87(2):117-25. Segal E, Widom J. What controls nucleosome positions? Trends Genet. 2009 Aug;25(8):335-43. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeBroadHmmNhlfHMM NHLF ChromHMM NHLF Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000792 792 GSM936086 Bernstein Broad hg18 ChromHMM_ENCODEDynamicPaper wgEncodeBroadHmmNhlfHMM HMM lung fibroblasts Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model NHLF Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmNhekHMM NHEK ChromHMM NHEK Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000791 791 GSM936087 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmNhekHMM HMM epidermal keratinocytes Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model NHEK Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmHsmmHMM HSMM ChromHMM HSMM Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000787 787 GSM936085 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmHsmmHMM HMM skeletal muscle myoblasts Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model HSMM Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmHmecHMM HMEC ChromHMM HMEC Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000786 786 GSM936084 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmHmecHMM HMM mammary epithelial cells Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model HMEC Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmHuvecHMM HUVEC ChromHMM HUVEC Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000788 788 GSM936089 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmHuvecHMM HMM umbilical vein endothelial cells Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model HUVEC Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmHepg2HMM HepG2 ChromHMM HepG2 Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000789 789 GSM936090 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmHepg2HMM HMM hepatocellular carcinoma Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model HepG2 Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmK562HMM K562 ChromHMM K562 Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000790 790 GSM936088 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmK562HMM HMM leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model K562 Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmH1hescHMM H1-hESC ChromHMM H1-hESC Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000785 785 GSM936083 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmH1hescHMM HMM embryonic stem cells Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model H1-hESC Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHmmGm12878HMM GM12878 ChromHMM GM12878 Combined ENCODE Mar 2012 Freeze 2011-03-16 2011-03-16 wgEncodeEH000784 784 GSM936082 Bernstein Broad hg18 ChromHMM_ENCODEDynamicsPaper wgEncodeBroadHmmGm12878HMM HMM B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Multi-assay Synthesis Bernstein Bernstein - Broad Institute Hidden Markov Model GM12878 Chromatin State Segmentation by HMM from ENCODE/Broad Regulation 
wgEncodeBroadHistone Broad Histone 2012-06-30 GSE29611 Histone Modifications by ChIP-seq from ENCODE/Broad Institute Regulation Description This track displays maps of chromatin state generated by the Broad/MGH ENCODE group using ChIP-seq. Chemical modifications (methylation, acetylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription. The ChIP-seq method involves first using formaldehyde to cross-link histones and other DNA-associated proteins to genomic DNA within cells. The cross-linked chromatin is subsequently extracted, mechanically sheared, and immunoprecipitated using specific antibodies. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. ENCODE tracks typically contain one or more of the following views: Peaks Regions of statistically significant signal enrichment. The score associated with each enriched interval is the mean signal value across the interval. (Note that a broad region with moderate enrichment may deviate from the background more significantly than a short region with high signal.) Signal Density graph (wiggle) of signal enrichment. At each base-pair position, the density is calculated as the number of sequenced tags overlapping a 25 bp window centered at that position. Peaks and signals displayed in this track are the results of pooled replicates. The raw sequence and alignment files for each replicate are available for download. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods ChIP-seq: Cells were grown according to the approved ENCODE cell culture protocols. Cells were fixed in 1% formaldehyde and resuspended in lysis buffer. Chromatin was sheared to 200-700 bp using a Diagenode Bioruptor. Solubilized chromatin was immunoprecipitated with antibodies against each of the histone antibodies listed above. Antibody-chromatin complexes were pulled down using protein A-sepharose (or anti-IgM-conjugated agarose for RNA polymerase II), washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, treated with RNAse and purified. A quantity of 1-10 ng of DNA was end-repaired, adapter-ligated and sequenced by Illumina Genome Analyzers as recommended by the manufacturer. Alignment: Sequence reads from each IP experiment were aligned to the human reference genome (GRCh37/hg19) using MAQ with default parameters, except '-C 11' and '-H output_file' were added. These options output up to 11 additional best matches for each read (if any are found) to a file. This information was used to filter out any read that had more than 10 best matches on the genome. Note that it is likely that instances where multiple reads align to the same position and with the same orientation are due to enhanced PCR amplification of a single DNA fragment. No attempt has been made, however, to remove such artifacts from the data, following ENCODE practices. Signal: Fragment densities were computed by counting the number of reads overlapping each 25 bp bin along the genome. Densities were computed using igvtools count with default parameters (in particular, '-w 25' to set window size of 25 bp and '-f mean' to report the mean value across the window), except for '-e' which was set to extend the reads to 200 bp, and the .wig output was converted to bigWig using wigToBigWig from the UCSC Kent software package. Peaks: Discrete intervals of ChIP-seq fragment enrichment were identified using Scripture, a scan statistics approach, under the assumption of uniform background signal. All data sets were processed with '-task chip', and with '-windows 100,200,500,1000,5000,10000,100000' (no mask file nor the '-trim' option have been used). The resulting called segments were then further filtered to remove intervals that were significantly enriched only because they contain smaller enriched intervals within them. This post-processing step has been implemented using Matlab. The use of the post-processing step allowed very large enriched intervals (of the order of Mbps for H3K27me3, for instance) to be detected, as well as much smaller intervals, without the need to tailor the parameters of Scripture based on prior expectations. Release Notes This is Release 3 (Aug 2012). It contains 83 new experiments including 6 new cell lines and 25 new antibodies. Please note that an antibody previously labeled "Pol2 (b)" is, in fact, Covance antibody MMS-128P with the target POLR2A. Credits The ChIP-seq data were generated at the Broad Institute and in the Bernstein lab at the Massachusetts General Hospital/Harvard Medical School.    Data generation and analysis were supported by funds from the NHGRI, the Burroughs Wellcome Fund, Massachusetts General Hospital and the Broad Institute. Contact: Noam Shoresh References Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ 3rd, Gingeras TR et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 2005 Jan 28;120(2):169-81. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006 Apr 21;125(2):315-26. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol. 2010 May;28(5):503-10. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007 Aug 2;448(7153):553-60. Publications Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011 Dec 23;147(7):1628-39. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until, above. The full data release policy for ENCODE is available here. 
wgEncodeBroadHistoneViewSignal Signal Histone Modifications by ChIP-seq from ENCODE/Broad Institute Regulation 
wgEncodeBroadHistoneOsteoblControlStdSig Osteobl Input Input Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001056 1056 GSM733697 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblControlStdSig None Signal osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoP300kat3bSig Osteobl P300 P300_KAT3B Osteobl std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003113 3113 GSM1003514 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneOsteoP300kat3bSig None Signal Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Osteoblasts P300 KAT3B Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH4k20me1Sig Osteobl H4K20m1 H4K20me1 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002401 2401 GSM1003467 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoH4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k79me2Sig Osteobl H3K79m2 H3K79me2 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002440 2440 GSM1003502 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k36me3StdSig Osteobl H3K36m3 H3K36me3 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001044 1044 GSM733721 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k27me3Sig Osteobl H3K27m3 H3K27me3 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002400 2400 GSM1003466 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoH3k27me3Sig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k27acStdSig Osteobl H3K27ac H3K27ac Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001043 1043 GSM733739 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k9me3StdSig Osteobl H3K9m3 H3K9me3 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001047 1047 GSM733681 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k9me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k04me3Sig Osteobl H3K4m3 H3K4me3 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003091 3091 GSM1003506 Bernstein Broad hg19 Illumina_GA2e exp wgEncodeBroadHistoneOsteoH3k04me3Sig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIe Signal Osteoblasts H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k4me2StdSig Osteobl H3K4m2 H3K4me2 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001046 1046 GSM733779 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k4me1StdSig Osteobl H3K4m1 H3K4me1 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001045 1045 GSM733704 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH2azStdSig Osteobl H2A.Z H2A.Z Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001042 1042 GSM733766 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblH2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblCtcfStdSig Osteobl CTCF CTCF Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001041 1041 GSM733784 Bernstein Broad hg19 exp wgEncodeBroadHistoneOsteoblCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Osteoblasts CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfControlStdSig NHLF Input Input NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000105 105 GSM733731 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfControlStdSig None Signal lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH4k20me1StdSig NHLF H4K20m1 H4K20me1 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000104 104 GSM733706 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k79me2Sig NHLF H3K79m2 H3K79me2 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002439 2439 GSM1003549 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhlfH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k36me3StdSig NHLF H3K36m3 H3K36me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000099 99 GSM733699 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k27me3StdSig NHLF H3K27m3 H3K27me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-29 wgEncodeEH000098 98 GSM733764 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k27acStdSig NHLF H3K27ac H3K27ac NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000097 97 GSM733646 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k09me3Sig NHLF H3K9m3 H3K9me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002424 2424 GSM1003531 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhlfH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k9acStdSig NHLF H3K9ac H3K9ac NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000103 103 GSM733652 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me3StdSig NHLF H3K4m3 H3K4me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000102 102 GSM733723 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me2StdSig NHLF H3K4m2 H3K4me2 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000101 101 GSM733781 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me1StdSig NHLF H3K4m1 H3K4me1 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000100 100 GSM733649 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH2azSig NHLF H2A.Z H2A.Z NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002423 2423 GSM1003530 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhlfH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfEzh239875Sig NHLF EZH2 EZH2_(39875) NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002422 2422 GSM1003529 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhlfEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfCtcfStdSig NHLF CTCF CTCF NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000120 120 GSM733695 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhlfCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHLF CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekControlStdSig NHEK Input Input NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000072 72 GSM733740 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekControlStdSig None Signal epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekPol2bStdSig NHEK Pol2 Pol2(b) NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000073 73 GSM733671 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekPol2bStdSig None Signal RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK Pol2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH4k20me1StdSig NHEK H4K20m1 H4K20me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000071 71 GSM733728 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k79me2Sig NHEK H3K79m2 H3K79me2 NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002420 2420 GSM1003527 Bernstein Broad hg19 exp M wgEncodeBroadHistoneNhekH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Signal NHEK H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k36me3StdSig NHEK H3K36m3 H3K36me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000066 66 GSM733726 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k27me3StdSig NHEK H3K27m3 H3K27me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000065 65 GSM733701 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k27acStdSig NHEK H3K27ac H3K27ac NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000064 64 GSM733674 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k9me1StdSig NHEK H3K9m1 H3K9me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000070 70 GSM733655 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k9me1StdSig None Signal Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K9me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k09me3Sig NHEK H3K9m3 H3K9me3 NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002421 2421 GSM1003528 Bernstein Broad hg19 exp M wgEncodeBroadHistoneNhekH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Signal NHEK H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k9acStdSig NHEK H3K9ac H3K9ac NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000069 69 GSM733665 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me3StdSig NHEK H3K4m3 H3K4me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000068 68 GSM733720 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me2StdSig NHEK H3K4m2 H3K4me2 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000067 67 GSM733686 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me1StdSig NHEK H3K4m1 H3K4me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000062 62 GSM733698 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH2azSig NHEK H2A.Z H2A.Z NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002419 2419 GSM1003488 Bernstein Broad hg19 exp M wgEncodeBroadHistoneNhekH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Signal NHEK H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekEzh239875Sig NHEK EZH2 EZH2_(39875) NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002418 2418 GSM1003489 Bernstein Broad hg19 exp M wgEncodeBroadHistoneNhekEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Signal NHEK EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekCtcfStdSig NHEK CTCF CTCF NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-07 2009-10-07 wgEncodeEH000063 63 GSM733636 Bernstein Broad hg18 exp wgEncodeBroadHistoneNhekCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHEK CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadControlStdSig NHDF-Ad Input Input NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001055 1055 GSM733750 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadControlStdSig None Signal adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH4k20me1Sig NHDF-Ad H4K20m1 H4K20me1 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002417 2417 GSM1003486 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k79me2Sig NHDF-Ad H3K79m2 H3K79me2 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002430 2430 GSM1003554 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k36me3StdSig NHDF-Ad H3K36m3 H3K36me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001051 1051 GSM733733 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k27me3StdSig NHDF-Ad H3K27m3 H3K27me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001050 1050 GSM733745 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k27acStdSig NHDF-Ad H3K27ac H3K27ac NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001049 1049 GSM733662 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k09me3Sig NHDF-Ad H3K9m3 H3K9me3 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002431 2431 GSM1003553 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k9acStdSig NHDF-Ad H3K9ac H3K9ac NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001054 1054 GSM733709 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k4me3StdSig NHDF-Ad H3K4m3 H3K4me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001053 1053 GSM733650 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k4me2StdSig NHDF-Ad H3K4m2 H3K4me2 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001052 1052 GSM733753 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k04me1Sig NHDF-Ad H3K4m1 H3K4me1 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002429 2429 GSM1003526 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadH3k04me1Sig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH2azSig NHDF-Ad H2A.Z H2A.Z NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003090 3090 GSM1003505 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneNhdfadH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal NHDF-Ad H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadEzh239875Sig NHDF-Ad EZH2 EZH2_(39875) NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002438 2438 GSM1003550 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadCtcfStdSig NHDF-Ad CTCF CTCF NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001048 1048 GSM733744 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhdfadCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NHDF-Ad CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaControlStdSig NH-A Input Input NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001027 1027 GSM733678 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaControlStdSig None Signal astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH4k20me1Sig NH-A H4K20m1 H4K20me1 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002428 2428 GSM1003525 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k79me2Sig NH-A H3K79m2 H3K79me2 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002398 2398 GSM1003490 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k36me3StdSig NH-A H3K36m3 H3K36me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001030 1030 GSM733751 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k27me3StdSig NH-A H3K27m3 H3K27me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001029 1029 GSM733729 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k27acStdSig NH-A H3K27ac H3K27ac NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001028 1028 GSM733763 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k09me3Sig NH-A H3K9m3 H3K9me3 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002399 2399 GSM1003491 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k09acSig NH-A H3K9ac H3K9ac NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002427 2427 GSM1003534 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k09acSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k4me3StdSig NH-A H3K4m3 H3K4me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001032 1032 GSM733747 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k04me2Sig NH-A H3K4m2 H3K4me2 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002426 2426 GSM1003533 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k04me2Sig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k4me1StdSig NH-A H3K4m1 H3K4me1 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001031 1031 GSM733710 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH2azSig NH-A H2A.Z H2A.Z NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002397 2397 GSM1003499 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaEzh239875Sig NH-A EZH2 EZH2_(39875) NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002425 2425 GSM1003532 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaCtcfStdSig NH-A CTCF CTCF NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH001026 1026 GSM733765 Bernstein Broad hg19 exp wgEncodeBroadHistoneNhaCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal NH-A CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtControlStdSig HSMMtube Input Input HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001001 1001 GSM733648 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtControlStdSig None Signal skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH4k20me1StdSig HSMMtube H4K20m1 H4K20me1 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001010 1010 GSM733644 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k79me2StdSig HSMMtube H3K79m2 H3K79me2 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001008 1008 GSM733727 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k36me3StdSig HSMMtube H3K36m3 H3K36me3 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001004 1004 GSM733717 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k27me3Sig HSMMtube H3K27m3 H3K27me3 HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH003092 3092 GSM1003503 Bernstein Broad hg19 Illumina_GA2e exp wgEncodeBroadHistoneHsmmtH3k27me3Sig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIe Signal HSMMtube H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k27acStdSig HSMMtube H3K27ac H3K27ac HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001003 1003 GSM733666 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k09me3Sig HSMMtube H3K9m3 H3K9me3 HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002394 2394 GSM1003482 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k9acStdSig HSMMtube H3K9ac H3K9ac HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001009 1009 GSM733639 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me3StdSig HSMMtube H3K4m3 H3K4me3 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001007 1007 GSM733738 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me2StdSig HSMMtube H3K4m2 H3K4me2 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001006 1006 GSM733700 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me1StdSig HSMMtube H3K4m1 H3K4me1 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001005 1005 GSM733661 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH2azStdSig HSMMtube H2A.Z H2A.Z HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001002 1002 GSM733746 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtH2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtEzh239875Sig HSMMtube EZH2 EZH2_(39875) HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003083 3083 GSM1003523 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHsmmtEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HSMMtube EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtCtcfStdSig HSMMtube CTCF CTCF HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001000 1000 GSM733783 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmtCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMMtube CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmControlStdSig HSMM Input Input HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000119 119 GSM733663 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmControlStdSig None Signal skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH4k20me1StdSig HSMM H4K20m1 H4K20me1 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000118 118 GSM733676 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k79me2StdSig HSMM H3K79m2 H3K79me2 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000998 998 GSM733741 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmH3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k36me3StdSig HSMM H3K36m3 H3K36me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000113 113 GSM733702 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k27me3StdSig HSMM H3K27m3 H3K27me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000112 112 GSM733667 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k27acStdSig HSMM H3K27ac H3K27ac HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000111 111 GSM733755 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k9me3StdSig HSMM H3K9m3 H3K9me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000999 999 GSM733730 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmH3k9me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k9acStdSig HSMM H3K9ac H3K9ac HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000117 117 GSM733775 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me3StdSig HSMM H3K4m3 H3K4me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000116 116 GSM733637 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me2StdSig HSMM H3K4m2 H3K4me2 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000115 115 GSM733768 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me1StdSig HSMM H3K4m1 H3K4me1 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000114 114 GSM733761 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH2azStdSig HSMM H2A.Z H2A.Z HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001036 1036 GSM733760 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmH2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmEzh239875Sig HSMM EZH2 EZH2_(39875) HSMM std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002415 2415 GSM1003484 Bernstein Broad hg19 exp wgEncodeBroadHistoneHsmmEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmCtcfStdSig HSMM CTCF CTCF HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000110 110 GSM733762 Bernstein Broad hg18 exp wgEncodeBroadHistoneHsmmCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HSMM CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecControlStdSig HMEC Input Input HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000093 93 GSM733668 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecControlStdSig None Signal mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH4k20me1StdSig HMEC H4K20m1 H4K20me1 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000092 92 GSM733647 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k79me2Sig HMEC H3K79m2 H3K79me2 HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002435 2435 GSM1003557 Bernstein Broad hg19 exp wgEncodeBroadHistoneHmecH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k36me3StdSig HMEC H3K36m3 H3K36me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000078 78 GSM733707 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k27me3StdSig HMEC H3K27m3 H3K27me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000077 77 GSM733722 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k27acStdSig HMEC H3K27ac H3K27ac HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000076 76 GSM733660 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k09me3Sig HMEC H3K9m3 H3K9me3 HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002414 2414 GSM1003485 Bernstein Broad hg19 exp wgEncodeBroadHistoneHmecH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k9acStdSig HMEC H3K9ac H3K9ac HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000079 79 GSM733713 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me3StdSig HMEC H3K4m3 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-29 wgEncodeEH000091 91 GSM733712 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me2StdSig HMEC H3K4m2 H3K4me2 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000090 90 GSM733654 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me1StdSig HMEC H3K4m1 H3K4me1 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000089 89 GSM733705 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH2azSig HMEC H2A.Z H2A.Z HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002413 2413 GSM1003500 Bernstein Broad hg19 exp wgEncodeBroadHistoneHmecH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecEzh239875Sig HMEC EZH2 EZH2_(39875) HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002412 2412 GSM1003501 Bernstein Broad hg19 exp wgEncodeBroadHistoneHmecEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecCtcfStdSig HMEC CTCF CTCF HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-27 wgEncodeEH000075 75 GSM733724 Bernstein Broad hg18 exp wgEncodeBroadHistoneHmecCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HMEC CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41ControlStdSig Dnd41 Input Input Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002434 2434 GSM1003558 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41ControlStdSig None Signal T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H4k20me1Sig Dnd41 H4K20m1 H4K20me1 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002410 2410 GSM1003481 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k79me2Sig Dnd41 H3K79m2 H3K79me2 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002409 2409 GSM1003469 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k36me3Sig Dnd41 H3K36m3 H3K36me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002405 2405 GSM1003463 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k36me3Sig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k27me3Sig Dnd41 H3K27m3 H3K27me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003081 3081 GSM1003521 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneDnd41H3k27me3Sig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal Dnd41 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k27acSig Dnd41 H3K27ac H3K27ac Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002404 2404 GSM1003462 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k27acSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k09me3Sig Dnd41 H3K9m3 H3K9me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002433 2433 GSM1003551 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k09acSig Dnd41 H3K9ac H3K9ac Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002432 2432 GSM1003552 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k09acSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me3Sig Dnd41 H3K4m3 H3K4me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002408 2408 GSM1003468 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k04me3Sig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me2Sig Dnd41 H3K4m2 H3K4me2 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002407 2407 GSM1003461 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k04me2Sig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me1Sig Dnd41 H3K4m1 H3K4me1 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002406 2406 GSM1003460 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H3k04me1Sig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H2azSig Dnd41 H2A.Z H2A.Z Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002403 2403 GSM1003465 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41H2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41Ezh239875Sig Dnd41 EZH2 EZH2_(39875) Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003080 3080 GSM1003522 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneDnd41Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal Dnd41 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41CtcfSig Dnd41 CTCF CTCF Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002402 2402 GSM1003464 Bernstein Broad hg19 exp wgEncodeBroadHistoneDnd41CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Dnd41 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746ControlSig CD14+ Control Control Monocytes-CD14+_RO01746 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003130 3130 GSM1003475 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneMonocd14ro1746ControlSig None Signal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Monocytes CD14+ Control Histone Mods by ChIPseq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H4k20me1Sig CD14+ H4K20m1 H4K20me1 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003074 3074 GSM1003539 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k79me2Sig CD14+ H3K79m2 H3K79me2 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003072 3072 GSM1003537 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k36me3Sig CD14+ H3K36m3 H3K36me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003069 3069 GSM1003562 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k36me3Sig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k27me3Sig CD14+ H3K27m3 H3K27me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003068 3068 GSM1003564 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k27me3Sig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k27acSig CD14+ H3K27ac H3K27ac Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003067 3067 GSM1003559 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k27acSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k09me3Sig CD14+ H3K9m3 H3K9me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003073 3073 GSM1003538 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k09acSig CD14+ H3K9ac H3K9ac Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003089 3089 GSM1003515 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneMonocd14ro1746H3k09acSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Monocytes CD14+ H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me3Sig CD14+ H3K4m3 H3K4me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003071 3071 GSM1003536 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k04me3Sig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me2Sig CD14+ H3K4m2 H3K4me2 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003088 3088 GSM1003516 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneMonocd14ro1746H3k04me2Sig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Monocytes CD14+ H3K4me2 Histone Mods by ChIPseq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me1Sig CD14+ H3K4m1 H3K4me1 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003070 3070 GSM1003535 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H3k04me1Sig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H2azSig CD14+ H2A.Z H2A.Z Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003066 3066 GSM1003548 Bernstein Broad hg19 exp wgEncodeBroadHistoneMonocd14ro1746H2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal Monocytes CD14+ H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746CtcfSig CD14+ CTCF CTCF Monocytes-CD14+_RO01746 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003097 3097 GSM1003508 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneMonocd14ro1746CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal Monocytes CD14+ CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecControlStdSig HUVEC Input Input HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000060 60 GSM733715 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecControlStdSig None Signal umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecPol2bStdSig HUVEC Pol2 Pol2(b) HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000061 61 GSM733749 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecPol2bStdSig None Signal RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC Pol2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH4k20me1StdSig HUVEC H4K20m1 H4K20me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000059 59 GSM733640 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k79me2Sig HUVEC H3K79m2 H3K79me2 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002437 2437 GSM1003555 Bernstein Broad hg19 exp wgEncodeBroadHistoneHuvecH3k79me2Sig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k36me3StdSig HUVEC H3K36m3 H3K36me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-26 2009-01-06 2009-10-06 wgEncodeEH000056 56 GSM733757 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k27me3StdSig HUVEC H3K27m3 H3K27me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000038 38 GSM733688 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k27acStdSig HUVEC H3K27ac H3K27ac HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000055 55 GSM733691 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k9me1StdSig HUVEC H3K9m1 H3K9me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000058 58 GSM733703 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k9me1StdSig None Signal Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K9me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k09me3Sig HUVEC H3K9m3 H3K9me3 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003085 3085 GSM1003517 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHuvecH3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HUVEC H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k9acStdSig HUVEC H3K9ac H3K9ac HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000057 57 GSM733735 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me3StdSig HUVEC H3K4m3 H3K4me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000041 41 GSM733673 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me2StdSig HUVEC H3K4m2 H3K4me2 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000040 40 GSM733683 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me1StdSig HUVEC H3K4m1 H3K4me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000039 39 GSM733690 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH2azSig HUVEC H2A.Z H2A.Z HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002436 2436 GSM1003556 Bernstein Broad hg19 exp wgEncodeBroadHistoneHuvecH2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecEzh239875Sig HUVEC EZH2 EZH2_(39875) HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003084 3084 GSM1003518 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHuvecEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HUVEC EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecCtcfStdSig HUVEC CTCF CTCF HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-06 2009-10-06 wgEncodeEH000054 54 GSM733716 Bernstein Broad hg18 exp wgEncodeBroadHistoneHuvecCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HUVEC CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2ControlStdSig HepG2 Input Input HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000084 84 GSM733732 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2ControlStdSig None Signal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H4k20me1StdSig HepG2 H4K20m1 H4K20me1 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000096 96 GSM733694 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k79me2StdSig HepG2 H3K79m2 H3K79me2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001024 1024 GSM733641 Bernstein Broad hg19 exp wgEncodeBroadHistoneHepg2H3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k36me3StdSig HepG2 H3K36m3 H3K36me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000081 81 GSM733685 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k27me3StdSig HepG2 H3K27m3 H3K27me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001023 1023 GSM733754 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k27acStdSig HepG2 H3K27ac H3K27ac HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000094 94 GSM733743 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k09me3Sig HepG2 H3K9m3 H3K9me3 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003087 3087 GSM1003519 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHepg2H3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HepG2 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k9acStdSig HepG2 H3K9ac H3K9ac HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000083 83 GSM733638 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k4me3StdSig HepG2 H3K4m3 H3K4me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000095 95 GSM733737 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k4me2StdSig HepG2 H3K4m2 H3K4me2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000082 82 GSM733693 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2H3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k04me1StdSig HepG2 H3K4m1 H3K4me1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2012-03-09 wgEncodeEH001749 1749 GSM798321 Bernstein Broad hg19 exp wgEncodeBroadHistoneHepg2H3k04me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H2azStdSig HepG2 H2A.Z H2A.Z HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001022 1022 GSM733774 Bernstein Broad hg19 exp wgEncodeBroadHistoneHepg2H2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2Ezh239875Sig HepG2 EZH2 EZH2_(39875) HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002416 2416 GSM1003487 Bernstein Broad hg19 exp wgEncodeBroadHistoneHepg2Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2CtcfStdSig HepG2 CTCF CTCF HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000080 80 GSM733645 Bernstein Broad hg18 exp wgEncodeBroadHistoneHepg2CtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HepG2 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3ControlStdSig HeLa-S3 Input Input HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001013 1013 GSM733659 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3ControlStdSig None Signal cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3Pol2bStdSig HeLa-S3 Pol2(b) Pol2(b) HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001021 1021 GSM733759 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3Pol2bStdSig None Signal RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 Pol2(b) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H4k20me1StdSig HeLa-S3 H4K20m1 H4K20me1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001020 1020 GSM733689 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k79me2StdSig HeLa-S3 H3K79m2 H3K79me2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001018 1018 GSM733669 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k36me3StdSig HeLa-S3 H3K36m3 H3K36me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001015 1015 GSM733711 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k27me3StdSig HeLa-S3 H3K27m3 H3K27me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001037 1037 GSM733696 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k27acStdSig HeLa-S3 H3K27ac H3K27ac HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001014 1014 GSM733684 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k09me3Sig HeLa-S3 H3K9m3 H3K9me3 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002396 2396 GSM1003480 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k09me3Sig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k9acStdSig HeLa-S3 H3K9ac H3K9ac HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001019 1019 GSM733756 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k4me3StdSig HeLa-S3 H3K4m3 H3K4me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001017 1017 GSM733682 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k4me2StdSig HeLa-S3 H3K4m2 H3K4me2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001016 1016 GSM733734 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k04me1StdSig HeLa-S3 H3K4m1 H3K4me1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-14 2012-03-14 wgEncodeEH001750 1750 GSM798322 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H3k04me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H2azSig HeLa-S3 H2A.Z H2A.Z HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002395 2395 GSM1003483 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3H2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3Ezh239875Sig HeLa-S3 EZH2 EZH2_(39875) HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003086 3086 GSM1003520 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneHelas3Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal HeLa-S3 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3CtcfStdSig HeLa-S3 CTCF CTCF HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH001012 1012 GSM733785 Bernstein Broad hg19 exp wgEncodeBroadHistoneHelas3CtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal HeLa-S3 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794H4k20me1Sig CD20+ H4K20m1 H4K20me1 CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003145 3145 GSM1003497 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20ro01794H4k20me1Sig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ RO01794 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794H3k27acSig CD20+ H3K27ac H3K27ac CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003125 3125 GSM1003459 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20ro01794H3k27acSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ RO01794 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794Ezh239875Sig CD20+ EZH2 EZH2_(39875) CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003135 3135 GSM1003470 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20ro01794Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ RO01794 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ControlSig CD20+ Control Control CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003132 3132 GSM1003477 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20ControlSig None Signal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ Control Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20H3k04me2Sig CD20+ H3K4m2 H3K4me2 CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003134 3134 GSM1003471 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20H3k04me2Sig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20H2azSig CD20+ H2A.Z H2A.Z CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003133 3133 GSM1003476 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20H2azSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20CtcfSig CD20+ CTCF CTCF CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003131 3131 GSM1003474 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneCd20CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal CD20+ CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549ControlEtoh02Sig A549 EtOH Control Control A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003076 3076 GSM1003541 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549ControlEtoh02Sig EtOH_0.02pct Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% Control Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549ControlDex100nmSig A549 DEX Control Control A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003075 3075 GSM1003540 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549ControlDex100nmSig DEX_100nM Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM Control Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H4k20me1Etoh02Sig A549 EtOH H4K20m1 H4K20me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003124 3124 GSM1003458 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H4k20me1Etoh02Sig EtOH_0.02pct Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k79me2Etoh02Sig A549 EtOH H3K79m2 H3K79me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003099 3099 GSM1003512 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k79me2Etoh02Sig EtOH_0.02pct Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k79me2Dex100nmSig A549 DEX H3K79m2 H3K79me2 A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003078 3078 GSM1003543 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k79me2Dex100nmSig DEX_100nM Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k36me3Etoh02Sig A549 EtOH H3K36m3 H3K36me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003121 3121 GSM1003456 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k36me3Etoh02Sig EtOH_0.02pct Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k36me3Dex100nmSig A549 DEX H3K36m3 H3K36me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003142 3142 GSM1003494 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k36me3Dex100nmSig DEX_100nM Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27me3Etoh02Sig A549 EtOH H3K27m3 H3K27me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003120 3120 GSM1003455 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k27me3Etoh02Sig EtOH_0.02pct Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27me3Dex100nmSig A549 DEX H3K27m3 H3K27me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003119 3119 GSM1003577 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k27me3Dex100nmSig DEX_100nM Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27acEtoh02Sig A549 EtOH H3K27ac H3K27ac A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003118 3118 GSM1003578 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k27acEtoh02Sig EtOH_0.02pct Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27acDex100nmSig A549 DEX H3K27ac H3K27ac A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003141 3141 GSM1003493 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k27acDex100nmSig DEX_100nM Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k09me3Etoh02Sig A549 EtOH H3K9m3 H3K9me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003123 3123 GSM1003454 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k09me3Etoh02Sig EtOH_0.02pct Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k09acEtoh02Sig A549 EtOH H3K9ac H3K9ac A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003079 3079 GSM1003544 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k09acEtoh02Sig EtOH_0.02pct Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me3Etoh02Sig A549 EtOH H3K4m3 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003065 3065 GSM1003561 Bernstein Broad hg19 exp wgEncodeBroadHistoneA549H3k04me3Etoh02Sig EtOH_0.02pct Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me3Dex100nmSig A549 DEX H3K4m3 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003077 3077 GSM1003542 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me3Dex100nmSig DEX_100nM Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me2Etoh02Sig A549 EtOH H3K4m2 H3K4me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003144 3144 GSM1003496 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me2Etoh02Sig EtOH_0.02pct Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me2Dex100nmSig A549 DEX H3K4m2 H3K4me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003098 3098 GSM1003511 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me2Dex100nmSig DEX_100nM Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me1Etoh02Sig A549 EtOH H3K4m1 H3K4me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003122 3122 GSM1003453 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me1Etoh02Sig EtOH_0.02pct Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me1Dex100nmSig A549 DEX H3K4m1 H3K4me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003143 3143 GSM1003495 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H3k04me1Dex100nmSig DEX_100nM Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H2azEtoh02Sig A549 EtOH H2A.Z H2A.Z A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003117 3117 GSM1003546 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H2azEtoh02Sig EtOH_0.02pct Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H2azDex100nmSig A549 DEX H2A.Z H2A.Z A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003116 3116 GSM1003580 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549H2azDex100nmSig DEX_100nM Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549CtcfEtoh02Sig A549 EtOH CTCF CTCF A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003115 3115 GSM1003581 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549CtcfEtoh02Sig EtOH_0.02pct Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Signal A549 EtOH 0.02% CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549CtcfDex100nmSig A549 DEX CTCF CTCF A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003114 3114 GSM1003582 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneA549CtcfDex100nmSig DEX_100nM Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Signal A549 DEX 100 nM CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562ControlStdSig K562 Input Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000052 52 GSM733780 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562ControlStdSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Suz12051317Sig K562 SUZ12 SUZ12_(05-1317) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003112 3112 GSM1003545 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Suz12051317Sig None Signal SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 SUZ12 (05-1317) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Sirt6Sig K562 SIRT6 SIRT6 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003111 3111 GSM1003560 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Sirt6Sig None Signal A synthetic peptide made to an internal region of the human SIRT6 protein leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 SIRT6 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Setdb1Sig K562 SETDB1 SETDB1 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003129 3129 GSM1003452 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Setdb1Sig None Signal SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 SETDB1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Sap3039731StdSig K562 SAP30 SAP30_(39731) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002094 2094 GSM1003445 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Sap3039731StdSig None Signal SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 SAP30 (39731) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Rnf2Sig K562 RNF2 RNF2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003110 3110 GSM1003563 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Rnf2Sig None Signal Ring finger protein 2 (RNF2) is a polycomb group (PcG) protein. RNF2 has been shown to interact with, and suppress the activity of, transcription factor CP2 (TFCP2/CP2). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 RNF2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562RestSig K562 REST REST K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003096 3096 GSM1003507 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562RestSig None Signal A transcriptional repressor which represses neuronal genes in non-neuronal tissues. A member of the Kruppel-type zinc finger transcription factor family. Represses transcription by binding a DNA sequence element called the neuron-restrictive silencer element (NRSE) by associating with two corepressors, mSin3 and CoREST, which recruit HDACs to the promoters of REST-regulated genes. Target is GST fusion amino acids 801-1097 of human REST. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 REST Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Rbbp5a300109aStdSig K562 RBBP5 RBBP5_(A300-109A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002093 2093 GSM1003449 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Rbbp5a300109aStdSig None Signal Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 RBBP5 (A300-109A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Pol2bStdSig K562 Pol2 Pol2(b) K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000053 53 GSM733643 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562Pol2bStdSig None Signal RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 Pol2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Plu1StdSig K562 PLU1 PLU1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-06-30 wgEncodeEH002085 2085 GSM1003586 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Plu1StdSig None Signal JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 PLU1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Phf8a301772aStdSig K562 PHF8 PHF8_(A301-772A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002092 2092 GSM1003450 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Phf8a301772aStdSig None Signal PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 PHF8 (A301-772A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562PcafSig K562 PCAF PCAF K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003109 3109 GSM1003566 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562PcafSig None Signal PCAF (P300/CBP-associated factor) is a histone acetyltransferase (HAT) identified as a factor that associates with P300/CBP, a transcriptional coactivator of nuclear hormone receptors and other transcription factors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 PCAF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562P300StdSig K562 P300 p300 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-06-30 wgEncodeEH002086 2086 GSM1003583 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562P300StdSig None Signal EP300(c-20) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 P300 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Nsd2ab75359Sig K562 NSD2 NSD2_(ab75359) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003140 3140 GSM1003492 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Nsd2ab75359Sig None Signal This is a probable histone methyltransferase, which may act as a transcription regulator that binds DNA and suppresses IL5 transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 NSD2 (ab75359) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562NcorSig K562 NCoR NCoR K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003108 3108 GSM1003565 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562NcorSig None Signal The nuclear receptor corepressor protein (NCoR) mediates gene repression by interacting with nuclear receptors. NCoR mediates repression by associating with SIN3A/B and the histone deacetylases, HDAC1 and HDAC2, and promoting the formation of repressive chromatin structures. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 NCoR Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Lsd1Sig K562 LSD1 LSD1 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003107 3107 GSM1003570 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Lsd1Sig None Signal BHC110/LSD1 is a histone demethylase and a component of several histone deacetylase complexes. BHC110/LSD1 is able to specifically catalyze the demethylation of Lys4 of histone H3. As part of histone deacetylase complexes BHC110/LSD1 functions as a corepressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 LSD1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac6a301341aSig K562 HDAC6 HDAC6_(A301-341A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003093 3093 GSM1003504 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Hdac6a301341aSig None Signal Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 HDAC6 (A301-341A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac2a300705aStdSig K562 HDAC2 HDAC2_(A300-705A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002091 2091 GSM1003447 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Hdac2a300705aStdSig None Signal Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 HDAC2 (A300-705A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac1sc6298StdSig K562 HDAC1 HDAC1_(SC-6298) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002090 2090 GSM1003448 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Hdac1sc6298StdSig None Signal Histone deacetylase 1 (HDAC1) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC1 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC1 include RPD3L1, HD1, GON-10, and DKFZp686H12203. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 HDAC1 (SC-6298) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H4k20me1StdSig K562 H4K20m1 H4K20me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000051 51 GSM733675 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k79me2StdSig K562 H3K79m2 H3K79me2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001039 1039 GSM733653 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562H3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k36me3StdSig K562 H3K36m3 H3K36me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000045 45 GSM733714 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k27me3StdSig K562 H3K27m3 H3K27me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000044 44 GSM733658 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k27acStdSig K562 H3K27ac H3K27ac K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000043 43 GSM733656 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9me1StdSig K562 H3K9m1 H3K9me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000050 50 GSM733777 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k9me1StdSig None Signal Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K9me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9me3StdSig K562 H3K9m3 H3K9me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001040 1040 GSM733776 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562H3k9me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9acStdSig K562 H3K9ac H3K9ac K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000049 49 GSM733778 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me3StdSig K562 H3K4m3 H3K4me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000048 48 GSM733680 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me2StdSig K562 H3K4m2 H3K4me2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000047 47 GSM733651 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me1StdSig K562 H3K4m1 H3K4me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000046 46 GSM733692 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562H3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H2azStdSig K562 H2A.Z H2A.Z K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001038 1038 GSM733786 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562H2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Ezh239875StdSig K562 EZH2 EZH2_(39875) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002089 2089 GSM1003576 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Ezh239875StdSig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562CtcfStdSig K562 CTCF CTCF K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000042 42 GSM733719 Bernstein Broad hg18 exp wgEncodeBroadHistoneK562CtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd7a301223a1Sig K562 CHD7 CHD7_(A301-223A-1) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003139 3139 GSM1003478 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Chd7a301223a1Sig None Signal CHD7 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 CHD7 (A301-223A-1) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd4mi2Sig K562 CHD4 Mi2 CHD4_Mi2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003095 3095 GSM1003510 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Chd4mi2Sig None Signal CHD4/Mi2beta is a helicase component of the nucleosome remodeling and deacetylase (NuRD) complex that functions to remodel chromatin and repress transcription. Outside of the NuRD complex, CHD4/Mi2beta can function as an activator of transcription in association with p300 histone acetyltransferase. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 CHD4 Mi2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd1a301218aStdSig K562 CHD1 CHD1_(A301-218A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002088 2088 GSM1003575 Bernstein Broad hg19 exp wgEncodeBroadHistoneK562Chd1a301218aStdSig None Signal CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal K562 CHD1 (A301-218A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx8Sig K562 CBX8 CBX8 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003106 3106 GSM1003569 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Cbx8Sig None Signal CBX8 is part of the polycomb group of proteins that are important in embryogenesis and human tumorigenesis and regulates a number of genes involved in cell growth and survival. There are at least 5 CBX proteins in mammals. CBX proteins associate with the core polycomb repressive complex 1 (PRC1) that functions to maintain the transcriptionally repressive state of genes during development. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 CBX8 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx3sc101004Sig K562 CBX3 CBX3_(SC-101004) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003105 3105 GSM1003568 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Cbx3sc101004Sig None Signal At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 CBX3 (SC-101004) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx2Sig K562 CBX2 CBX2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003104 3104 GSM1003567 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneK562Cbx2Sig None Signal Chromobox protein homolog 2 is a component of the polycomb group (PcG) multiprotein PRC1 complex, a complex required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. [taken from the Universal Protein Resource (UniProt) www.uniprot.org/uniprot/P19474] leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal K562 CBX2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbpsc369Sig K562 CBP (SC-369) CBP_(sc-369) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003103 3103 GSM1003574 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneK562Cbpsc369Sig None Signal CBP is a histone acetyl transferase that promotes transcription. CBP is recruited by a variety of transcription factors to promoters and enhancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal K562 CBP (sc-369) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescControlStdSig H1-hESC Input Input H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000088 88 GSM733770 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescControlStdSig None Signal embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSuz12051317Sig H1-hESC SUZ12 SUZ12_(05-1317) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003102 3102 GSM1003573 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescSuz12051317Sig None Signal SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC SUZ12 (05-1317) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSirt6Sig H1-hESC SIRT6 SIRT6 H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003128 3128 GSM1003451 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescSirt6Sig None Signal A synthetic peptide made to an internal region of the human SIRT6 protein embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC SIRT6 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSap3039731Sig H1-hESC SAP30 SAP30_(39731) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003101 3101 GSM1003572 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescSap3039731Sig None Signal SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC SAP30 (39731) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescRbbp5a300109aStdSig H1-hESC RBBP5 RBBP5_(A300-109A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002087 2087 GSM1003584 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescRbbp5a300109aStdSig None Signal Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC RBBP5 (A300-109A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescPlu1Sig H1-hESC PLU1 PLU1 H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003127 3127 GSM1003457 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescPlu1Sig None Signal JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC PLU1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescPhf8a301772aSig H1-hESC PHF8 PHF8_(A301-772A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003094 3094 GSM1003509 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescPhf8a301772aSig None Signal PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC PHF8 (A301-772A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescP300kat3bSig H1-hESC P300 P300_KAT3B H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003126 3126 GSM1003513 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescP300kat3bSig None Signal Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC P300 KAT3B Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescJmjd2aa300861a1Sig H1-hESC JMJD2A JMJD2A_(A300-861A-1) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003138 3138 GSM1003479 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescJmjd2aa300861a1Sig None Signal JMJD2A is a member of the jumonji (jmj) domain containing gene family of histone demethylases that plays a role in chromatin regulation and influences transcriptional activation and suppression. JMJD2A is a trimethylation-specific demethylase and functions as a transcriptional repressor. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC JMJD2A (A300-861A-1) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescJarid1aab26049StdSig H1-hESC JARID1A JARID1A_(ab26049) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002096 2096 GSM1003446 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescJarid1aab26049StdSig None Signal Histone demethylase that specifically demethylates embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC JARID1A (ab26049) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescHdac6a301341aSig H1-hESC HDAC6 HDAC6_(A301-341A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003100 3100 GSM1003571 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescHdac6a301341aSig None Signal Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC HDAC6 (A301-341A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescHdac2a300705aSig H1-hESC HDAC2 HDAC2_(A300-705A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003137 3137 GSM1003472 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescHdac2a300705aSig None Signal Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC HDAC2 (A300-705A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH4k20me1StdSig H1-hESC H4K20m1 H4K20me1 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-29 wgEncodeEH000087 87 GSM733687 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k79me2StdSig H1-hESC H3K79m2 H3K79me2 H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002083 2083 GSM1003547 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescH3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k36me3StdSig H1-hESC H3K36m3 H3K36me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000107 107 GSM733725 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k27me3StdSig H1-hESC H3K27m3 H3K27me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-28 2010-06-28 wgEncodeEH000074 74 GSM733748 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k27me3StdSig None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k27acStdSig H1-hESC H3K27ac H3K27ac H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-06-21 2011-03-21 wgEncodeEH000997 997 GSM733718 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescH3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k09me3StdSig H1-hESC H3K9m3 H3K9me3 H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002084 2084 GSM1003585 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescH3k09me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k9acStdSig H1-hESC H3K9ac H3K9ac H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000109 109 GSM733773 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me3StdSig H1-hESC H3K4m3 H3K4me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-28 wgEncodeEH000086 86 GSM733657 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k4me3StdSig None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me2StdSig H1-hESC H3K4m2 H3K4me2 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-12-16 2010-09-16 wgEncodeEH000108 108 GSM733670 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me1StdSig H1-hESC H3K4m1 H3K4me1 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-30 2010-06-30 wgEncodeEH000106 106 GSM733782 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescH3k4me1StdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH2azStdSig H1-hESC H2A.Z H2A.Z H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-04 2012-05-04 wgEncodeEH002082 2082 GSM1003579 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescH2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescEzh239875Sig H1-hESC EZH2 EZH2_(39875) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003082 3082 GSM1003524 Bernstein Broad hg19 Illumina_HiSeq_2000 exp wgEncodeBroadHistoneH1hescEzh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Signal H1-hESC EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescCtcfStdSig H1-hESC CTCF CTCF H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-09-29 2010-06-29 wgEncodeEH000085 85 GSM733672 Bernstein Broad hg18 exp wgEncodeBroadHistoneH1hescCtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescChd7a301223a1Sig H1-hESC CHD7 CHD7_(A301-223A-1) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003136 3136 GSM1003473 Bernstein Broad hg19 Illumina_GA2x exp wgEncodeBroadHistoneH1hescChd7a301223a1Sig None Signal CHD7 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Signal H1-hESC CHD7 (A301-223A-1) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescChd1a301218aStdSig H1-hESC CHD1 CHD1_(A301-218A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002095 2095 GSM1003444 Bernstein Broad hg19 exp wgEncodeBroadHistoneH1hescChd1a301218aStdSig None Signal CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal H1-hESC CHD1 (A301-218A) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878ControlStdSig GM12878 Input Input GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-07-12 2011-04-12 wgEncodeEH000037 37 GSM733742 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878ControlStdSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 Input Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H4k20me1StdSig GM12878 H4K20m1 H4K20me1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000036 36 GSM733642 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H4k20me1StdSig None Signal Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H4K20me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k79me2StdSig GM12878 H3K79m2 H3K79me2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001034 1034 GSM733736 Bernstein Broad hg19 exp wgEncodeBroadHistoneGm12878H3k79me2StdSig None Signal H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k36me3StdSig GM12878 H3K36m3 H3K36me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000032 32 GSM733679 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k36me3StdSig None Signal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k27me3StdSigV2 GM12878 H3K27m3 H3K27me3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2009-10-05 wgEncodeEH000031 31 GSM733758 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k27me3StdSigV2 None Signal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k27acStdSig GM12878 H3K27ac H3K27ac GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000030 30 GSM733771 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k27acStdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k9me3StdSig GM12878 H3K9m3 H3K9me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001035 1035 GSM733664 Bernstein Broad hg19 exp wgEncodeBroadHistoneGm12878H3k9me3StdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k9acStdSig GM12878 H3K9ac H3K9ac GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000035 35 GSM733677 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k9acStdSig None Signal Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k04me3StdSigV2 GM12878 H3K4m3 H3K4me3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2009-10-04 wgEncodeEH000028 28 GSM733708 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k04me3StdSigV2 None Signal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k4me2StdSig GM12878 H3K4m2 H3K4me2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000034 34 GSM733769 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k4me2StdSig None Signal Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k04me1StdSigV2 GM12878 H3K4m1 H3K4me1 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2009-10-05 wgEncodeEH000033 33 GSM733772 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878H3k04me1StdSigV2 None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H2azStdSig GM12878 H2A.Z H2A.Z GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001033 1033 GSM733767 Bernstein Broad hg19 exp wgEncodeBroadHistoneGm12878H2azStdSig None Signal H2A.Z (H2AFZ) is a sequence variant of Histone H2A. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 H2A.Z Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878Ezh239875Sig GM12878 EZH2 EZH2_(39875) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002411 2411 GSM1003498 Bernstein Broad hg19 exp wgEncodeBroadHistoneGm12878Ezh239875Sig None Signal EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 EZH2 (39875) Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878CtcfStdSig GM12878 CTCF CTCF GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2009-01-05 2009-10-05 wgEncodeEH000029 29 GSM733752 Bernstein Broad hg18 exp wgEncodeBroadHistoneGm12878CtcfStdSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Signal GM12878 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad Regulation 
wgEncodeBroadHistoneViewPeaks Peaks Histone Modifications by ChIP-seq from ENCODE/Broad Institute Regulation 
wgEncodeBroadHistoneOsteoP300kat3bPk Osteobl P300 P300_KAT3B Osteobl std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003113 3113 GSM1003514 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoP300kat3bPk None Peaks Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment Osteoblasts P300 KAT3B Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH4k20me1Pk Osteobl H4K20m1 H4K20me1 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002401 2401 GSM1003467 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoH4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k79me2Pk Osteobl H3K79m2 H3K79me2 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002440 2440 GSM1003502 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k36me3StdPk Osteobl H3K36m3 H3K36me3 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001044 1044 GSM733721 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k27me3Pk Osteobl H3K27m3 H3K27me3 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002400 2400 GSM1003466 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoH3k27me3Pk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k27acStdPk Osteobl H3K27ac H3K27ac Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001043 1043 GSM733739 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k9me3StdPk Osteobl H3K9m3 H3K9me3 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001047 1047 GSM733681 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k9me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoH3k04me3Pk Osteobl H3K4m3 H3K4me3 Osteobl std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003091 3091 GSM1003506 Bernstein Broad hg19 Illumina_GA2e exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoH3k04me3Pk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIe Regions of enriched signal in experiment Osteoblasts H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k4me2StdPk Osteobl H3K4m2 H3K4me2 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001046 1046 GSM733779 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH3k4me1StdPk Osteobl H3K4m1 H3K4me1 Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001045 1045 GSM733704 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblH2azStdPk Osteobl H2A.Z H2A.Z Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001042 1042 GSM733766 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblH2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneOsteoblCtcfStdPk Osteobl CTCF CTCF Osteobl std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001041 1041 GSM733784 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneOsteoblCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. osteoblasts (NHOst) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Osteoblasts CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH4k20me1StdPk NHLF H4K20m1 H4K20me1 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000104 104 GSM733706 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k79me2Pk NHLF H3K79m2 H3K79me2 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002439 2439 GSM1003549 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k36me3StdPk NHLF H3K36m3 H3K36me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000099 99 GSM733699 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k27me3StdPk NHLF H3K27m3 H3K27me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000098 98 GSM733764 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k27acStdPk NHLF H3K27ac H3K27ac NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000097 97 GSM733646 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k09me3Pk NHLF H3K9m3 H3K9me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002424 2424 GSM1003531 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k9acStdPk NHLF H3K9ac H3K9ac NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000103 103 GSM733652 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me3StdPk NHLF H3K4m3 H3K4me3 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000102 102 GSM733723 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me2StdPk NHLF H3K4m2 H3K4me2 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000101 101 GSM733781 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH3k4me1StdPk NHLF H3K4m1 H3K4me1 NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000100 100 GSM733649 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfH2azPk NHLF H2A.Z H2A.Z NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002423 2423 GSM1003530 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfEzh239875Pk NHLF EZH2 EZH2_(39875) NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002422 2422 GSM1003529 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhlfCtcfStdPk NHLF CTCF CTCF NHLF std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000120 120 GSM733695 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhlfCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHLF CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekPol2bStdPk NHEK Pol2 Pol2(b) NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000073 73 GSM733671 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekPol2bStdPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK Pol2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH4k20me1StdPk NHEK H4K20m1 H4K20me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000071 71 GSM733728 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k79me2Pk NHEK H3K79m2 H3K79me2 NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002420 2420 GSM1003527 Bernstein Broad hg19 exp M ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Regions of enriched signal in experiment NHEK H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k36me3StdPk NHEK H3K36m3 H3K36me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000066 66 GSM733726 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k27me3StdPk NHEK H3K27m3 H3K27me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000065 65 GSM733701 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k27acStdPk NHEK H3K27ac H3K27ac NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000064 64 GSM733674 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k9me1StdPk NHEK H3K9m1 H3K9me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000070 70 GSM733655 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k9me1StdPk None Peaks Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K9me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k09me3Pk NHEK H3K9m3 H3K9me3 NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002421 2421 GSM1003528 Bernstein Broad hg19 exp M ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Regions of enriched signal in experiment NHEK H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k9acStdPk NHEK H3K9ac H3K9ac NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000069 69 GSM733665 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me3StdPk NHEK H3K4m3 H3K4me3 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000068 68 GSM733720 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me2StdPk NHEK H3K4m2 H3K4me2 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000067 67 GSM733686 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH3k4me1StdPk NHEK H3K4m1 H3K4me1 NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000062 62 GSM733698 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekH2azPk NHEK H2A.Z H2A.Z NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002419 2419 GSM1003488 Bernstein Broad hg19 exp M ScriptureVPaperR3 wgEncodeBroadHistoneNhekH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Regions of enriched signal in experiment NHEK H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekEzh239875Pk NHEK EZH2 EZH2_(39875) NHEK std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002418 2418 GSM1003489 Bernstein Broad hg19 exp M ScriptureVPaperR3 wgEncodeBroadHistoneNhekEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Male Regions of enriched signal in experiment NHEK EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhekCtcfStdPk NHEK CTCF CTCF NHEK std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000063 63 GSM733636 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhekCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHEK CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH4k20me1Pk NHDF-Ad H4K20m1 H4K20me1 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002417 2417 GSM1003486 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k79me2Pk NHDF-Ad H3K79m2 H3K79me2 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002430 2430 GSM1003554 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k36me3StdPk NHDF-Ad H3K36m3 H3K36me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001051 1051 GSM733733 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k27me3StdPk NHDF-Ad H3K27m3 H3K27me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001050 1050 GSM733745 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k27acStdPk NHDF-Ad H3K27ac H3K27ac NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001049 1049 GSM733662 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k09me3Pk NHDF-Ad H3K9m3 H3K9me3 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002431 2431 GSM1003553 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k9acStdPk NHDF-Ad H3K9ac H3K9ac NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001054 1054 GSM733709 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k4me3StdPk NHDF-Ad H3K4m3 H3K4me3 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001053 1053 GSM733650 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k4me2StdPk NHDF-Ad H3K4m2 H3K4me2 NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001052 1052 GSM733753 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH3k04me1Pk NHDF-Ad H3K4m1 H3K4me1 NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002429 2429 GSM1003526 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH3k04me1Pk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadH2azPk NHDF-Ad H2A.Z H2A.Z NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003090 3090 GSM1003505 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment NHDF-Ad H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadEzh239875Pk NHDF-Ad EZH2 EZH2_(39875) NHDF-Ad std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002438 2438 GSM1003550 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhdfadCtcfStdPk NHDF-Ad CTCF CTCF NHDF-Ad std ChipSeq ENCODE Jan 2011 Freeze 2010-11-19 2011-08-19 wgEncodeEH001048 1048 GSM733744 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhdfadCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NHDF-Ad CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH4k20me1Pk NH-A H4K20m1 H4K20me1 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002428 2428 GSM1003525 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k79me2Pk NH-A H3K79m2 H3K79me2 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002398 2398 GSM1003490 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k36me3StdPk NH-A H3K36m3 H3K36me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001030 1030 GSM733751 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k27me3StdPk NH-A H3K27m3 H3K27me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001029 1029 GSM733729 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k27acStdPk NH-A H3K27ac H3K27ac NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001028 1028 GSM733763 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k09me3Pk NH-A H3K9m3 H3K9me3 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002399 2399 GSM1003491 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k09acPk NH-A H3K9ac H3K9ac NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002427 2427 GSM1003534 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k09acPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k4me3StdPk NH-A H3K4m3 H3K4me3 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001032 1032 GSM733747 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k04me2Pk NH-A H3K4m2 H3K4me2 NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002426 2426 GSM1003533 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k04me2Pk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH3k4me1StdPk NH-A H3K4m1 H3K4me1 NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001031 1031 GSM733710 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaH2azPk NH-A H2A.Z H2A.Z NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002397 2397 GSM1003499 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaEzh239875Pk NH-A EZH2 EZH2_(39875) NH-A std ChipSeq ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002425 2425 GSM1003532 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneNhaCtcfStdPk NH-A CTCF CTCF NH-A std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001026 1026 GSM733765 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneNhaCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes (also called Astrocy) Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment NH-A CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH4k20me1StdPk HSMMtube H4K20m1 H4K20me1 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001010 1010 GSM733644 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k79me2StdPk HSMMtube H3K79m2 H3K79me2 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001008 1008 GSM733727 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k36me3StdPk HSMMtube H3K36m3 H3K36me3 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001004 1004 GSM733717 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k27me3Pk HSMMtube H3K27m3 H3K27me3 HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH003092 3092 GSM1003503 Bernstein Broad hg19 Illumina_GA2e exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k27me3Pk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIe Regions of enriched signal in experiment HSMMtube H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k27acStdPk HSMMtube H3K27ac H3K27ac HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001003 1003 GSM733666 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k09me3Pk HSMMtube H3K9m3 H3K9me3 HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002394 2394 GSM1003482 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k9acStdPk HSMMtube H3K9ac H3K9ac HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001009 1009 GSM733639 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me3StdPk HSMMtube H3K4m3 H3K4me3 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001007 1007 GSM733738 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me2StdPk HSMMtube H3K4m2 H3K4me2 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001006 1006 GSM733700 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH3k4me1StdPk HSMMtube H3K4m1 H3K4me1 HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001005 1005 GSM733661 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtH2azStdPk HSMMtube H2A.Z H2A.Z HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001002 1002 GSM733746 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtH2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtEzh239875Pk HSMMtube EZH2 EZH2_(39875) HSMMtube std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003083 3083 GSM1003523 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HSMMtube EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmtCtcfStdPk HSMMtube CTCF CTCF HSMMtube std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001000 1000 GSM733783 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmtCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myotubes differentiated from the HSMM cell line Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMMtube CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH4k20me1StdPk HSMM H4K20m1 H4K20me1 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000118 118 GSM733676 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k79me2StdPk HSMM H3K79m2 H3K79me2 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000998 998 GSM733741 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k36me3StdPk HSMM H3K36m3 H3K36me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000113 113 GSM733702 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k27me3StdPk HSMM H3K27m3 H3K27me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000112 112 GSM733667 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k27acStdPk HSMM H3K27ac H3K27ac HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000111 111 GSM733755 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k9me3StdPk HSMM H3K9m3 H3K9me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000999 999 GSM733730 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k9me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k9acStdPk HSMM H3K9ac H3K9ac HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000117 117 GSM733775 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me3StdPk HSMM H3K4m3 H3K4me3 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000116 116 GSM733637 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me2StdPk HSMM H3K4m2 H3K4me2 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000115 115 GSM733768 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH3k4me1StdPk HSMM H3K4m1 H3K4me1 HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000114 114 GSM733761 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmH2azStdPk HSMM H2A.Z H2A.Z HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001036 1036 GSM733760 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmH2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmEzh239875Pk HSMM EZH2 EZH2_(39875) HSMM std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002415 2415 GSM1003484 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHsmmCtcfStdPk HSMM CTCF CTCF HSMM std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000110 110 GSM733762 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHsmmCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skeletal muscle myoblasts Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HSMM CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH4k20me1StdPk HMEC H4K20m1 H4K20me1 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000092 92 GSM733647 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k79me2Pk HMEC H3K79m2 H3K79me2 HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002435 2435 GSM1003557 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k36me3StdPk HMEC H3K36m3 H3K36me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000078 78 GSM733707 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k27me3StdPk HMEC H3K27m3 H3K27me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000077 77 GSM733722 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k27acStdPk HMEC H3K27ac H3K27ac HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000076 76 GSM733660 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k09me3Pk HMEC H3K9m3 H3K9me3 HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002414 2414 GSM1003485 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k9acStdPk HMEC H3K9ac H3K9ac HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000079 79 GSM733713 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me3StdPk HMEC H3K4m3 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000091 91 GSM733712 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me2StdPk HMEC H3K4m2 H3K4me2 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000090 90 GSM733654 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH3k4me1StdPk HMEC H3K4m1 H3K4me1 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000089 89 GSM733705 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecH2azPk HMEC H2A.Z H2A.Z HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-20 wgEncodeEH002413 2413 GSM1003500 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecEzh239875Pk HMEC EZH2 EZH2_(39875) HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002412 2412 GSM1003501 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHmecCtcfStdPk HMEC CTCF CTCF HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000075 75 GSM733724 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHmecCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HMEC CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H4k20me1Pk Dnd41 H4K20m1 H4K20me1 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002410 2410 GSM1003481 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k79me2Pk Dnd41 H3K79m2 H3K79me2 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002409 2409 GSM1003469 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k36me3Pk Dnd41 H3K36m3 H3K36me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002405 2405 GSM1003463 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k36me3Pk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k27me3Pk Dnd41 H3K27m3 H3K27me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003081 3081 GSM1003521 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k27me3Pk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment Dnd41 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k27acPk Dnd41 H3K27ac H3K27ac Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002404 2404 GSM1003462 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k27acPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k09me3Pk Dnd41 H3K9m3 H3K9me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002433 2433 GSM1003551 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k09acPk Dnd41 H3K9ac H3K9ac Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002432 2432 GSM1003552 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k09acPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me3Pk Dnd41 H3K4m3 H3K4me3 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002408 2408 GSM1003468 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k04me3Pk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me2Pk Dnd41 H3K4m2 H3K4me2 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002407 2407 GSM1003461 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k04me2Pk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H3k04me1Pk Dnd41 H3K4m1 H3K4me1 Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002406 2406 GSM1003460 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H3k04me1Pk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41H2azPk Dnd41 H2A.Z H2A.Z Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002403 2403 GSM1003465 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41H2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41Ezh239875Pk Dnd41 EZH2 EZH2_(39875) Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003080 3080 GSM1003522 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment Dnd41 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneDnd41CtcfPk Dnd41 CTCF CTCF Dnd41 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002402 2402 GSM1003464 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneDnd41CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. T cell leukemia with Notch mutation Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Dnd41 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H4k20me1Pk CD14+ H4K20m1 H4K20me1 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003074 3074 GSM1003539 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k79me2Pk CD14+ H3K79m2 H3K79me2 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003072 3072 GSM1003537 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k36me3Pk CD14+ H3K36m3 H3K36me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003069 3069 GSM1003562 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k36me3Pk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k27me3Pk CD14+ H3K27m3 H3K27me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003068 3068 GSM1003564 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k27me3Pk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k27acPk CD14+ H3K27ac H3K27ac Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003067 3067 GSM1003559 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k27acPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k09me3Pk CD14+ H3K9m3 H3K9me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003073 3073 GSM1003538 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k09acPk CD14+ H3K9ac H3K9ac Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003089 3089 GSM1003515 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k09acPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment Monocytes CD14+ H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me3Pk CD14+ H3K4m3 H3K4me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003071 3071 GSM1003536 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k04me3Pk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me2Pk CD14+ H3K4m2 H3K4me2 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003088 3088 GSM1003516 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k04me2Pk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment Monocytes CD14+ H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H3k04me1Pk CD14+ H3K4m1 H3K4me1 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003070 3070 GSM1003535 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H3k04me1Pk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746H2azPk CD14+ H2A.Z H2A.Z Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003066 3066 GSM1003548 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746H2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment Monocytes CD14+ H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneMonocd14ro1746CtcfPk CD14+ CTCF CTCF Monocytes-CD14+_RO01746 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003097 3097 GSM1003508 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneMonocd14ro1746CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment Monocytes CD14+ CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecPol2bStdPk HUVEC Pol2 Pol2(b) HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000061 61 GSM733749 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecPol2bStdPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC Pol2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH4k20me1StdPk HUVEC H4K20m1 H4K20me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000059 59 GSM733640 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k79me2Pk HUVEC H3K79m2 H3K79me2 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002437 2437 GSM1003555 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k79me2Pk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k36me3StdPk HUVEC H3K36m3 H3K36me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-12 2011-05-05 wgEncodeEH000056 56 GSM733757 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k27me3StdPk HUVEC H3K27m3 H3K27me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000038 38 GSM733688 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k27acStdPk HUVEC H3K27ac H3K27ac HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000055 55 GSM733691 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k9me1StdPk HUVEC H3K9m1 H3K9me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000058 58 GSM733703 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k9me1StdPk None Peaks Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K9me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k09me3Pk HUVEC H3K9m3 H3K9me3 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003085 3085 GSM1003517 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HUVEC H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k9acStdPk HUVEC H3K9ac H3K9ac HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000057 57 GSM733735 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me3StdPk HUVEC H3K4m3 H3K4me3 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000041 41 GSM733673 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me2StdPk HUVEC H3K4m2 H3K4me2 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000040 40 GSM733683 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH3k4me1StdPk HUVEC H3K4m1 H3K4me1 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000039 39 GSM733690 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecH2azPk HUVEC H2A.Z H2A.Z HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2012-07-25 wgEncodeEH002436 2436 GSM1003556 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecH2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecEzh239875Pk HUVEC EZH2 EZH2_(39875) HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003084 3084 GSM1003518 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HUVEC EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHuvecCtcfStdPk HUVEC CTCF CTCF HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000054 54 GSM733716 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHuvecCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HUVEC CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H4k20me1StdPk HepG2 H4K20m1 H4K20me1 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000096 96 GSM733694 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k79me2StdPk HepG2 H3K79m2 H3K79me2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001024 1024 GSM733641 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k36me3StdPk HepG2 H3K36m3 H3K36me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000081 81 GSM733685 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k27me3StdPk HepG2 H3K27m3 H3K27me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH001023 1023 GSM733754 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k27acStdPk HepG2 H3K27ac H3K27ac HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000094 94 GSM733743 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k09me3Pk HepG2 H3K9m3 H3K9me3 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003087 3087 GSM1003519 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HepG2 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k9acStdPk HepG2 H3K9ac H3K9ac HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000083 83 GSM733638 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k4me3StdPk HepG2 H3K4m3 H3K4me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000095 95 GSM733737 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k4me2StdPk HepG2 H3K4m2 H3K4me2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000082 82 GSM733693 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H3k04me1StdPk HepG2 H3K4m1 H3K4me1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2012-03-09 wgEncodeEH001749 1749 GSM798321 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H3k04me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2H2azStdPk HepG2 H2A.Z H2A.Z HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH001022 1022 GSM733774 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2H2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2Ezh239875Pk HepG2 EZH2 EZH2_(39875) HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002416 2416 GSM1003487 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHepg2CtcfStdPk HepG2 CTCF CTCF HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000080 80 GSM733645 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneHepg2CtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HepG2 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3Pol2bStdPk HeLa-S3 Pol2 Pol2(b) HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001021 1021 GSM733759 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3Pol2bStdPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 Pol2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H4k20me1StdPk HeLa-S3 H4K20m1 H4K20me1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001020 1020 GSM733689 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k79me2StdPk HeLa-S3 H3K79m2 H3K79me2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001018 1018 GSM733669 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k36me3StdPk HeLa-S3 H3K36m3 H3K36me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001015 1015 GSM733711 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k27me3StdPk HeLa-S3 H3K27m3 H3K27me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001037 1037 GSM733696 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k27acStdPk HeLa-S3 H3K27ac H3K27ac HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001014 1014 GSM733684 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k09me3Pk HeLa-S3 H3K9m3 H3K9me3 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002396 2396 GSM1003480 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k09me3Pk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k9acStdPk HeLa-S3 H3K9ac H3K9ac HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001019 1019 GSM733756 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k4me3StdPk HeLa-S3 H3K4m3 H3K4me3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001017 1017 GSM733682 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k4me2StdPk HeLa-S3 H3K4m2 H3K4me2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001016 1016 GSM733734 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H3k04me1StdPk HeLa-S3 H3K4m1 H3K4me1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-14 2012-03-14 wgEncodeEH001750 1750 GSM798322 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H3k04me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3H2azPk HeLa-S3 H2A.Z H2A.Z HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-20 2012-07-20 wgEncodeEH002395 2395 GSM1003483 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3H2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3Ezh239875Pk HeLa-S3 EZH2 EZH2_(39875) HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003086 3086 GSM1003520 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment HeLa-S3 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneHelas3CtcfStdPk HeLa-S3 CTCF CTCF HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH001012 1012 GSM733785 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneHelas3CtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment HeLa-S3 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794H4k20me1Pk CD20+ H4K20m1 H4K20me1 CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003145 3145 GSM1003497 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20ro01794H4k20me1Pk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ RO01794 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794H3k27acPk CD20+ H3K27ac H3K27ac CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003125 3125 GSM1003459 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20ro01794H3k27acPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ RO01794 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20ro01794Ezh239875Pk CD20+ EZH2 EZH2_(39875) CD20+_RO01794 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003135 3135 GSM1003470 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20ro01794Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ RO01794 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20H3k04me2Pk CD20+ H3K4m2 H3K4me2 CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003134 3134 GSM1003471 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20H3k04me2Pk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20H2azPk CD20+ H2A.Z H2A.Z CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003133 3133 GSM1003476 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20H2azPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneCd20CtcfPk CD20+ CTCF CTCF CD20+ std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003131 3131 GSM1003474 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneCd20CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment CD20+ CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H4k20me1Etoh02Pk A549 EtOH H4K20m1 H4K20me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003124 3124 GSM1003458 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H4k20me1Etoh02Pk EtOH_0.02pct Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k79me2Etoh02Pk A549 EtOH H3K79m2 H3K79me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003099 3099 GSM1003512 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k79me2Etoh02Pk EtOH_0.02pct Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k79me2Dex100nmPk A549 DEX H3K79m2 H3K79me2 A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003078 3078 GSM1003543 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k79me2Dex100nmPk DEX_100nM Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k36me3Etoh02Pk A549 EtOH H3K36m3 H3K36me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003121 3121 GSM1003456 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k36me3Etoh02Pk EtOH_0.02pct Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k36me3Dex100nmPk A549 DEX H3K36m3 H3K36me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003142 3142 GSM1003494 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k36me3Dex100nmPk DEX_100nM Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27me3Etoh02Pk A549 EtOH H3K27m3 H3K27me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003120 3120 GSM1003455 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k27me3Etoh02Pk EtOH_0.02pct Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27me3Dex100nmPk A549 DEX H3K27m3 H3K27me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003119 3119 GSM1003577 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k27me3Dex100nmPk DEX_100nM Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27acEtoh02Pk A549 EtOH H3K27ac H3K27ac A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003118 3118 GSM1003578 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k27acEtoh02Pk EtOH_0.02pct Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k27acDex100nmPk A549 DEX H3K27ac H3K27ac A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003141 3141 GSM1003493 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k27acDex100nmPk DEX_100nM Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k09me3Etoh02Pk A549 EtOH H3K9m3 H3K9me3 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003123 3123 GSM1003454 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k09me3Etoh02Pk EtOH_0.02pct Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k09acEtoh02Pk A549 EtOH H3K9ac H3K9ac A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003079 3079 GSM1003544 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k09acEtoh02Pk EtOH_0.02pct Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me3Etoh02Pk A549 EtOH H3K4m3 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-11-04 2012-08-04 wgEncodeEH003065 3065 GSM1003561 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me3Etoh02Pk EtOH_0.02pct Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me3Dex100nmPk A549 DEX H3K4m3 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003077 3077 GSM1003542 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me3Dex100nmPk DEX_100nM Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me2Etoh02Pk A549 EtOH H3K4m2 H3K4me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003144 3144 GSM1003496 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me2Etoh02Pk EtOH_0.02pct Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me2Dex100nmPk A549 DEX H3K4m2 H3K4me2 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003098 3098 GSM1003511 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me2Dex100nmPk DEX_100nM Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me1Etoh02Pk A549 EtOH H3K4m1 H3K4me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003122 3122 GSM1003453 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me1Etoh02Pk EtOH_0.02pct Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H3k04me1Dex100nmPk A549 DEX H3K4m1 H3K4me1 A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003143 3143 GSM1003495 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H3k04me1Dex100nmPk DEX_100nM Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H2azEtoh02Pk A549 EtOH H2A.Z H2A.Z A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003117 3117 GSM1003546 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H2azEtoh02Pk EtOH_0.02pct Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549H2azDex100nmPk A549 DEX H2A.Z H2A.Z A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003116 3116 GSM1003580 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549H2azDex100nmPk DEX_100nM Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549CtcfEtoh02Pk A549 EtOH CTCF CTCF A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003115 3115 GSM1003581 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549CtcfEtoh02Pk EtOH_0.02pct Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 EtOH 0.02% CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneA549CtcfDex100nmPk A549 DEX CTCF CTCF A549 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003114 3114 GSM1003582 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneA549CtcfDex100nmPk DEX_100nM Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 DEX 100 nM CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Suz12051317Pk K562 SUZ12 SUZ12_(05-1317) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003112 3112 GSM1003545 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Suz12051317Pk None Peaks SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 SUZ12 (05-1317) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Sirt6Pk K562 SIRT6 SIRT6 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003111 3111 GSM1003560 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Sirt6Pk None Peaks A synthetic peptide made to an internal region of the human SIRT6 protein leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 SIRT6 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Setdb1Pk K562 SETDB1 SETDB1 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003129 3129 GSM1003452 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Setdb1Pk None Peaks SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 SETDB1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Sap3039731StdPk K562 SAP30 SAP30_(39731) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002094 2094 GSM1003445 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Sap3039731StdPk None Peaks SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 SAP30 (39731) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Rnf2Pk K562 RNF2 RNF2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003110 3110 GSM1003563 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Rnf2Pk None Peaks Ring finger protein 2 (RNF2) is a polycomb group (PcG) protein. RNF2 has been shown to interact with, and suppress the activity of, transcription factor CP2 (TFCP2/CP2). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 RNF2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562RestPk K562 REST REST K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003096 3096 GSM1003507 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562RestPk None Peaks A transcriptional repressor which represses neuronal genes in non-neuronal tissues. A member of the Kruppel-type zinc finger transcription factor family. Represses transcription by binding a DNA sequence element called the neuron-restrictive silencer element (NRSE) by associating with two corepressors, mSin3 and CoREST, which recruit HDACs to the promoters of REST-regulated genes. Target is GST fusion amino acids 801-1097 of human REST. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 REST Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Rbbp5a300109aStdPk K562 RBBP5 RBBP5_(A300-109A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002093 2093 GSM1003449 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Rbbp5a300109aStdPk None Peaks Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 RBBP5 (A300-109A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Pol2bStdPk K562 Pol2 Pol2(b) K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000053 53 GSM733643 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Pol2bStdPk None Peaks RNA polymerase II. Is responsible for RNA transcription. It is generally enriched at 5' gene ends, probably due to higher rate of occupancy associated with transition from initiation to elongation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 Pol2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Plu1StdPk K562 PLU1 PLU1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-06-30 wgEncodeEH002085 2085 GSM1003586 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Plu1StdPk None Peaks JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 PLU1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Phf8a301772aStdPk K562 PHF8 PHF8_(A301-772A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002092 2092 GSM1003450 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Phf8a301772aStdPk None Peaks PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 PHF8 (A301-772A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562PcafPk K562 PCAF PCAF K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003109 3109 GSM1003566 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562PcafPk None Peaks PCAF (P300/CBP-associated factor) is a histone acetyltransferase (HAT) identified as a factor that associates with P300/CBP, a transcriptional coactivator of nuclear hormone receptors and other transcription factors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 PCAF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562P300StdPk K562 P300 p300 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-06-30 wgEncodeEH002086 2086 GSM1003583 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562P300StdPk None Peaks EP300(c-20) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 P300 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Nsd2ab75359Pk K562 NSD2 NSD2_(ab75359) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003140 3140 GSM1003492 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Nsd2ab75359Pk None Peaks This is a probable histone methyltransferase, which may act as a transcription regulator that binds DNA and suppresses IL5 transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 NSD2 (ab75359) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562NcorPk K562 NCoR NCoR K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003108 3108 GSM1003565 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562NcorPk None Peaks The nuclear receptor corepressor protein (NCoR) mediates gene repression by interacting with nuclear receptors. NCoR mediates repression by associating with SIN3A/B and the histone deacetylases, HDAC1 and HDAC2, and promoting the formation of repressive chromatin structures. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 NCoR Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Lsd1Pk K562 LSD1 LSD1 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003107 3107 GSM1003570 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Lsd1Pk None Peaks BHC110/LSD1 is a histone demethylase and a component of several histone deacetylase complexes. BHC110/LSD1 is able to specifically catalyze the demethylation of Lys4 of histone H3. As part of histone deacetylase complexes BHC110/LSD1 functions as a corepressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 LSD1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac6a301341aPk K562 HDAC6 HDAC6_(A301-341A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003093 3093 GSM1003504 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Hdac6a301341aPk None Peaks Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 HDAC6 (A301-341A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac2a300705aStdPk K562 HDAC2 HDAC2_(A300-705A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002091 2091 GSM1003447 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Hdac2a300705aStdPk None Peaks Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 HDAC2 (A300-705A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Hdac1sc6298StdPk K562 HDAC1 HDAC1_(SC-6298) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002090 2090 GSM1003448 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Hdac1sc6298StdPk None Peaks Histone deacetylase 1 (HDAC1) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC1 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC1 include RPD3L1, HD1, GON-10, and DKFZp686H12203. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 HDAC1 (SC-6298) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H4k20me1StdPk K562 H4K20m1 H4K20me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000051 51 GSM733675 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k79me2StdPk K562 H3K79m2 H3K79me2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001039 1039 GSM733653 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k36me3StdPk K562 H3K36m3 H3K36me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000045 45 GSM733714 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k27me3StdPk K562 H3K27m3 H3K27me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000044 44 GSM733658 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k27acStdPk K562 H3K27ac H3K27ac K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000043 43 GSM733656 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9me1StdPk K562 H3K9m1 H3K9me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000050 50 GSM733777 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k9me1StdPk None Peaks Histone H3 (mono-methyl K9). Is associated with active and accessible regions. NOTE CONTRAST to H3K9me3 which is associated with repressive heterochromatic state. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K9me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9me3StdPk K562 H3K9m3 H3K9me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001040 1040 GSM733776 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k9me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k9acStdPk K562 H3K9ac H3K9ac K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000049 49 GSM733778 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me3StdPk K562 H3K4m3 H3K4me3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000048 48 GSM733680 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me2StdPk K562 H3K4m2 H3K4me2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000047 47 GSM733651 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H3k4me1StdPk K562 H3K4m1 H3K4me1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000046 46 GSM733692 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562H2azStdPk K562 H2A.Z H2A.Z K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001038 1038 GSM733786 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562H2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Ezh239875StdPk K562 EZH2 EZH2_(39875) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002089 2089 GSM1003576 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Ezh239875StdPk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562CtcfStdPk K562 CTCF CTCF K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000042 42 GSM733719 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562CtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd7a301223a1Pk K562 CHD7 CHD7_(A301-223A-1) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003139 3139 GSM1003478 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Chd7a301223a1Pk None Peaks CHD7 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 CHD7 (A301-223A-1) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd4mi2Pk K562 CHD4 Mi2 CHD4_Mi2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003095 3095 GSM1003510 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Chd4mi2Pk None Peaks CHD4/Mi2beta is a helicase component of the nucleosome remodeling and deacetylase (NuRD) complex that functions to remodel chromatin and repress transcription. Outside of the NuRD complex, CHD4/Mi2beta can function as an activator of transcription in association with p300 histone acetyltransferase. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 CHD4 Mi2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Chd1a301218aStdPk K562 CHD1 CHD1_(A301-218A) K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002088 2088 GSM1003575 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Chd1a301218aStdPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment K562 CHD1 (A301-218A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx8Pk K562 CBX8 CBX8 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003106 3106 GSM1003569 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Cbx8Pk None Peaks CBX8 is part of the polycomb group of proteins that are important in embryogenesis and human tumorigenesis and regulates a number of genes involved in cell growth and survival. There are at least 5 CBX proteins in mammals. CBX proteins associate with the core polycomb repressive complex 1 (PRC1) that functions to maintain the transcriptionally repressive state of genes during development. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 CBX8 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx3sc101004Pk K562 CBX3 CBX3_(SC-101004) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003105 3105 GSM1003568 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Cbx3sc101004Pk None Peaks At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 CBX3 (SC-101004) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbx2Pk K562 CBX2 CBX2 K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003104 3104 GSM1003567 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Cbx2Pk None Peaks Chromobox protein homolog 2 is a component of the polycomb group (PcG) multiprotein PRC1 complex, a complex required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. [taken from the Universal Protein Resource (UniProt) www.uniprot.org/uniprot/P19474] leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment K562 CBX2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneK562Cbpsc369Pk K562 CBP (SC-369) CBP_(sc-369) K562 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003103 3103 GSM1003574 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneK562Cbpsc369Pk None Peaks CBP is a histone acetyl transferase that promotes transcription. CBP is recruited by a variety of transcription factors to promoters and enhancers. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment K562 CBP (sc-369) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSuz12051317Pk H1-hESC SUZ12 SUZ12_(05-1317) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003102 3102 GSM1003573 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescSuz12051317Pk None Peaks SUZ12 is a polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. They probably act via the methylation of histones, rendering chromatin heritably changed in its expressibility. This protein is component of the PRC2 complex, which methylates Lys-9 and Lys-27 residues of histone H3. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC SUZ12 (05-1317) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSirt6Pk H1-hESC SIRT6 SIRT6 H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003128 3128 GSM1003451 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescSirt6Pk None Peaks A synthetic peptide made to an internal region of the human SIRT6 protein embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC SIRT6 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescSap3039731Pk H1-hESC SAP30 SAP30_(39731) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-23 wgEncodeEH003101 3101 GSM1003572 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescSap3039731Pk None Peaks SAP30, also known asSin3A-associated protein, 30kDa, is part of the SIN3 corepressor complex, that also includes SIN3, SAP18,HDAC1,HDAC2,RbAp46andRbAp48. SAP30 is involved in the functional recruitment of the Sin3-histone deacetylase complex to a specific subset of N-CoR corepressor complexes. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC SAP30 (39731) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescRbbp5a300109aStdPk H1-hESC RBBP5 RBBP5_(A300-109A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002087 2087 GSM1003584 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescRbbp5a300109aStdPk None Peaks Retinoblastoma binding protein 5 (RbBP5) is a subunit of a human Set1-like histone methyltransferase (HMT) complex. The Set-1 like complexes are responsible for mono-, di-, and tri-methylation of histone H3 K4. RbBP5 associates with a multitude of proteins in a number of Set1-like complexes which include various combinations of MLL, MLL2, MLL3, MLL4, ASH2L,WDR5, hDPY-30, hSwd2, CXXC1, HCF1, Menin, PTIP, PA1, NCOA6, and UTX. RbBP5 is also one of many proteins that bind the Retinoblastoma tumor suppressor protein, pRb. Alternate names for RbBP5 are RBQ3 and SWD1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC RBBP5 (A300-109A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescPlu1Pk H1-hESC PLU1 PLU1 H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003127 3127 GSM1003457 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescPlu1Pk None Peaks JARID1B (Jumonji AT-rich interactive domain 1B) is a member of the JARID 1 family of proteins that catalyze the demethylation of histones on lysine. The Jarid 1 family members include JARID1A, JARID1B, JARID1C and JARID1D. The members of this family possess a Jumonji C (JmjC) and Jumonji N (JmjN) domain as well as one ARID (AT-rich interactive domain) and three PHD-type zinc fingers. As histone demethylases, JARID 1 proteins function as transcriptional repressors. JARID1B expression is largely restricted to testis and may play a critical role in tumorigenesis as it has been found to be upregulated in prostate and breast cancer. Alternative names for JARID1B include retinoblastoma-binding protein 2 homolog 1, RBP2-H1, cancer/testis antigen 31, CT31, PLU-1, PUT1, and KDM5B. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC PLU1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescPhf8a301772aPk H1-hESC PHF8 PHF8_(A301-772A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-23 wgEncodeEH003094 3094 GSM1003509 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescPhf8a301772aPk None Peaks PHF8 (PHD finger protein 8) is a member of the jumonji family of proteins and contains a jumonji C (JmjC) domain. The JmjC proteins are predicted to be metalloenzymes that play a role a chromatin remodeling and histone demethylation. PHF8 also bears a PHD (plant homeodomain)- type zinc-finger, a domain also found to be involved in chromatin remodeling and transcriptional regulation. Truncating mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 is also known as ZNF422 and KIAA1111. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC PHF8 (A301-772A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescP300kat3bPk H1-hESC P300 P300_KAT3B H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003126 3126 GSM1003513 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescP300kat3bPk None Peaks Histone acetyltransferase with sequence similarity to CBP (CREB-binding protein). Regulates transcription by influencing chromatin organization. P300 has been demonstrated to bind to phosphorylated CREB to mediate cAMP-gene regulation. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC P300 KAT3B Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescJmjd2aa300861a1Pk H1-hESC JMJD2A JMJD2A_(A300-861A-1) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003138 3138 GSM1003479 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescJmjd2aa300861a1Pk None Peaks JMJD2A is a member of the jumonji (jmj) domain containing gene family of histone demethylases that plays a role in chromatin regulation and influences transcriptional activation and suppression. JMJD2A is a trimethylation-specific demethylase and functions as a transcriptional repressor. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC JMJD2A (A300-861A-1) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescJarid1aab26049StdPk H1-hESC JARID1A JARID1A_(ab26049) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002096 2096 GSM1003446 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescJarid1aab26049StdPk None Peaks Histone demethylase that specifically demethylates embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC JARID1A (ab26049) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescHdac6a301341aPk H1-hESC HDAC6 HDAC6_(A301-341A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003100 3100 GSM1003571 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescHdac6a301341aPk None Peaks Histone deacetylase 6 (HDAC6) is a class II histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminus of core histones. HDAC6 has also been identified as a cytoplasmic deacetylase that acts on tubulin and HSP90 to influence cell motility. Recently HDAC6 has been found to be involved in the stress response as a component of cytoplasmic stress granules. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC HDAC6 (A301-341A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescHdac2a300705aPk H1-hESC HDAC2 HDAC2_(A300-705A) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003137 3137 GSM1003472 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescHdac2a300705aPk None Peaks Histone deacetylase 2 (HDAC2) is a class I histone deacetylase that catalyzes the removal of the acetyl group on lysine residues of the N-terminus of the core histones H2A, H2B, H3, and H4. HDAC2 is a component of multiple deacetylating complexes such as Sin3, NuRD, and CoRest that function to repress gene transcription. Alternate names for HDAC2 include HD2, RPD3, and YAF1. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC HDAC2 (A300-705A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH4k20me1StdPk H1-hESC H4K20m1 H4K20me1 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000087 87 GSM733687 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k79me2StdPk H1-hESC H3K79m2 H3K79me2 H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002083 2083 GSM1003547 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k36me3StdPk H1-hESC H3K36m3 H3K36me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000107 107 GSM733725 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k27me3StdPk H1-hESC H3K27m3 H3K27me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000074 74 GSM733748 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k27me3StdPk None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k27acStdPk H1-hESC H3K27ac H3K27ac H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000997 997 GSM733718 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k09me3StdPk H1-hESC H3K9m3 H3K9me3 H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002084 2084 GSM1003585 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k09me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k9acStdPk H1-hESC H3K9ac H3K9ac H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000109 109 GSM733773 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me3StdPk H1-hESC H3K4m3 H3K4me3 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000086 86 GSM733657 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k4me3StdPk None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me2StdPk H1-hESC H3K4m2 H3K4me2 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000108 108 GSM733670 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH3k4me1StdPk H1-hESC H3K4m1 H3K4me1 H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000106 106 GSM733782 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH3k4me1StdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescH2azStdPk H1-hESC H2A.Z H2A.Z H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-08-04 2012-05-04 wgEncodeEH002082 2082 GSM1003579 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescH2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescEzh239875Pk H1-hESC EZH2 EZH2_(39875) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-03-15 2012-12-15 wgEncodeEH003082 3082 GSM1003524 Bernstein Broad hg19 Illumina_HiSeq_2000 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescEzh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina HiSeq 2000 Regions of enriched signal in experiment H1-hESC EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescCtcfStdPk H1-hESC CTCF CTCF H1-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-08-05 wgEncodeEH000085 85 GSM733672 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescCtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescChd7a301223a1Pk H1-hESC CHD7 CHD7_(A301-223A-1) H1-hESC std ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEH003136 3136 GSM1003473 Bernstein Broad hg19 Illumina_GA2x exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescChd7a301223a1Pk None Peaks CHD7 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Illumina Genome Analyzer IIx Regions of enriched signal in experiment H1-hESC CHD7 (A301-223A-1) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneH1hescChd1a301218aStdPk H1-hESC CHD1 CHD1_(A301-218A) H1-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002095 2095 GSM1003444 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneH1hescChd1a301218aStdPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment H1-hESC CHD1 (A301-218A) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H4k20me1StdPk GM12878 H4K20m1 H4K20me1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000036 36 GSM733642 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H4k20me1StdPk None Peaks Histone H4 (mono-methyl K20). Is associated with active and accessible regions. In mammals, PR-Set7 specifically catalyzes H4K20 monomethylation. NOTE CONTRAST to H3K20me3 which is associated with heterochromatin and DNA repair. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H4K20me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k79me2StdPk GM12878 H3K79m2 H3K79me2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-08-15 wgEncodeEH001034 1034 GSM733736 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k79me2StdPk None Peaks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k36me3StdPk GM12878 H3K36m3 H3K36me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000032 32 GSM733679 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k36me3StdPk None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k27me3StdPkV2 GM12878 H3K27m3 H3K27me3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2011-08-05 wgEncodeEH000031 31 GSM733758 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k27me3StdPkV2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k27acStdPk GM12878 H3K27ac H3K27ac GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000030 30 GSM733771 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k27acStdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k9me3StdPk GM12878 H3K9m3 H3K9me3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001035 1035 GSM733664 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k9me3StdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k9acStdPk GM12878 H3K9ac H3K9ac GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000035 35 GSM733677 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k9acStdPk None Peaks Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k04me3StdPkV2 GM12878 H3K4m3 H3K4me3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2011-08-05 wgEncodeEH000028 28 GSM733708 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k04me3StdPkV2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k4me2StdPk GM12878 H3K4m2 H3K4me2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000034 34 GSM733769 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k4me2StdPk None Peaks Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H3k04me1StdPkV2 GM12878 H3K4m1 H3K4me1 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2011-08-05 wgEncodeEH000033 33 GSM733772 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H3k04me1StdPkV2 None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878H2azStdPk GM12878 H2A.Z H2A.Z GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-16 2011-05-05 wgEncodeEH001033 1033 GSM733767 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878H2azStdPk None Peaks H2A.Z (H2AFZ) is a sequence variant of Histone H2A. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 H2A.Z Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878Ezh239875Pk GM12878 EZH2 EZH2_(39875) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 2012-07-21 wgEncodeEH002411 2411 GSM1003498 Bernstein Broad hg19 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878Ezh239875Pk None Peaks EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 EZH2 (39875) Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeBroadHistoneGm12878CtcfStdPk GM12878 CTCF CTCF GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-11-05 2010-11-05 2011-05-05 wgEncodeEH000029 29 GSM733752 Bernstein Broad hg18 exp ScriptureVPaperR3 wgEncodeBroadHistoneGm12878CtcfStdPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Bernstein Bernstein - Broad Institute Regions of enriched signal in experiment GM12878 CTCF Histone Mods by ChIP-seq Peaks from ENCODE/Broad Regulation 
wgEncodeCaltechRnaSeq Caltech RNA-seq GSE33480 RNA-seq from ENCODE/Caltech Expression Description This track was produced as part of the ENCODE Project. RNA-seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly. RNA-seq was performed by reverse-transcribing an RNA sample into cDNA, followed by high-throughput DNA sequencing, which was done on an Illumina Genome Analyzer (GAI or GAIIx) (Mortazavi et al., 2008). The transcriptome measurements shown on these tracks were performed on polyA selected RNA from total cellular RNA using two different protocols: one that preserves information about which strand the read is coming from and one that does not. Due to the specifics of the enzymology of library construction, gene and transcript quantification is more accurate based on the non-strand-specific protocol, while the strand-specific protocol is useful for assigning strandedness, but in general less reliable for quantification. Non-strand-specific Protocol (deep "reference" transcriptome measurements, 2x75 bp reads) PolyA-selected RNA was fragmented by magnesium-catalyzed hydrolysis, converted into cDNA by random priming and then amplified. Data were produced in two formats: single reads, each of which came from one end of a cDNA molecule, and paired-end reads, which were obtained as pairs from both ends of cDNAs. This RNA-seq protocol does not specify the coding strand. As a result, there is ambiguity at loci where both strands are transcribed. The "randomly primed" reverse transcription is, apparently, not fully random. This is inferred from a sequence bias in the first residues of the read population, and this likely contributes to observed unevenness in sequence coverage across transcripts. Strand-specific Protocol (1x75 bp reads) PolyA-selected RNA was fragmented by magnesium-catalyzed hydrolysis. A set of 3' and 5' adapters were ligated to the 3' and 5' ends of the fragments, respectively. The resulting RNA molecules were converted to cDNA and amplified. This RNA-seq protocol does specify the coding strand as each read is in the same 5'-3' orientation as the original RNA strand. As a result, loci where both strands are transcribed can be disambiguated. However, RNA ligation is an inherently biased process and as a result, greater unevenness in sequence coverage across transcripts is observed compared to the non-strand-specific data, and quantification is less accurate. Data Analysis Reads were aligned to the hg19 human reference genome using TopHat (Trapnell et al., 2009), a program specifically designed to align RNA-seq reads and discover splice junctions de novo. Cufflinks (Trapnell et al., 2010), a de novo transcript assembly and quantification software package, was run on the TopHat alignments to discover and quantify novel transcripts and to obtain transcript expression estimates based on the GENCODE annotation. All sequence files, alignments, gene and transcript models and expression estimates files are available for download. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. The following views are in this track: Alignments The Alignments view shows reads aligned to the genome. Alignments are colored by cell type. The tags used in this file are: NH XS CP NM CC. The 'XS' custom tag indicates the sense/anti-sense of the strand. See the Bowtie Manual (Langmead et al., 2009) for more information about the SAM Bowtie output (including other tags) and the SAM Format Specification for more information on the SAM/BAM file format. For Stranded Data (1x75) Plus Raw Signal (only for stranded data) Density graph (wiggle) of signal enrichment based on a normalized aligned read density (Read Per Million, RPM) for reads aligning to the forward strand. Minus Raw Signal (only for stranded data) Density graph (wiggle) of signal enrichment based on a normalized aligned read density (Read Per Million, RPM) for reads aligning to the reverse strand. Minus strand score is multiplied by -1 for display purposes so that data can be viewed around an axis. For Paired-End Non-Stranded Data (2x75) Raw Signal (only for paired-end data) Density graph (wiggle) of signal enrichment based on a normalized aligned read density (Read Per Million, RPM). The RPM measure assists in visualizing the relative amount of a given transcript across multiple samples. A separate track for the forward (plus) and reverse (minus) strands are provided for strand-specific data. Splice Sites Subset of aligned reads that crosses splice junctions. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Experimental Procedures Cells were grown according to the approved ENCODE cell culture protocols except for H1-hESC for which frozen cell pellets were purchased from Cellular Dynamics. Cells were lysed in RLT buffer (Qiagen RNeasy kit) and processed on RNeasy midi columns according to the manufacturer's protocol, with the inclusion of the "on-column" DNase digestion step to remove residual genomic DNA. A quantity of 75 µg of total RNA was selected twice with oligo-dT beads (Dynal) according to the manufacturer's protocol to isolate mRNA from each of the preparations. For 2x75 bp non-stranded RNA-seq, 100 ng of mRNA was then processed according to the protocol in Mortazavi et al. (2008), and prepared for sequencing on the Genome Analyzer flow cell according to the protocol for the ChIP-seq DNA genomic DNA kit (Illumina). The majority of paired-end libraries were size-selected around 200 bp (fragment length) with the exception of a few additional replicates that were size-selected at 400 bp with the specific intent to investigate the effect of fragment length on results. Strand-specific RNA-seq libraries were prepared from 100 ng of mRNA from the same preparation following Illumina's Strand-Specific RNA-seq protocol. Libraries were sequenced with an Illumina Genome Analyzer I or an Illumina Genome Analyzer IIx according to the manufacturer's recommendations. Reads of 75 bp length were obtained, single-end for directional, strand-specific libraries (1x75D) and paired-end for non-strand-specific libraries (2x75). Data Processing and Analysis Reads were mapped to the reference human genome (version hg19), with or without the Y chromosome, depending on the sex of the cell line, and without the random chromosomes and haplotypes in all cases, using TopHat (version 1.0.14). TopHat was used with default settings with the exception of specifying an empirically determined mean inner-mate distance. After mapping reads to the genome and identifying splice junctions, the data were further analyzed using the transcript assembly and quantification software Cufflinks (version 0.9.3) using the sequence bias detection and correction option. Cufflinks was used in two modes: 1) expression for genes and individual transcripts was quantified based on the GENCODE annotation, for both versions v3c and v4 of GENCODE GRCh37; 2) Cufflinks was run in de novo transcript assembly and quantification mode to obtain candidate novel transcript and gene models and expression estimates for them. Downloadable Files The following files can be found on the downloads page: .fastq - Raw sequence files in fastq format with phred33 quality scores. Junctions.bedRnaElements - A BED file containing TopHat-defined splice junctions. TranscriptDeNovo.gtf - A GTF file containing transcript models and expression estimates in FPKM (Fragments Per Kilobase per Million reads) produced by Cufflinks in de novo mode. TranscriptGencV3c.gtf - Expression level estimates at the transcript level for the GENCODE GRCh37.v3c annotation in GTF format. GenesDeNovo.gtf - Expression estimates for genes defined by Cufflinks in de novo mode in GTF format. GeneGencV3c.gtf - Expression level estimates at the gene level for the GENCODE GRCh37.v3c annotation in GTF format. ExonGencV3c.gtf - Expression level estimates for GENCODE GRCh37.v3c exons in GTF format derived by summing the expression levels in FPKM for all transcripts containing a given exon. TSS.gtf - Expression level estimates for GENCODE GRCh37.v3c transcription start sites (TSS) in GTF format derived by summing the expression levels in FPKM for all transcripts originating from a given TSS. Verification Known exon maps as displayed on the genome browser are confirmed by the alignment of sequence reads. Known spliced exons are detected at the expected frequency for transcripts of given abundance. Linear range detection of spiked-in RNA transcripts from Arabidopsis and phage lambda over 5 orders of magnitude. Endpoint RT-PCR confirms presence of selected 3' UTR extensions. Correlation to published microarray data r = 0.62. Release Notes This is release 4 (August 2012). Fastq files for GM12892, GM12891 and K562 (R1x75) were replaced after errors were found in the GEO submission process. Credits Wold Group: Ali Mortazavi, Brian Williams, Georgi Marinov, Diane Trout, Brandon King, Ken McCue, Lorian Schaeffer. Myers Group: Norma Neff, Florencia Pauli, Fan Zhang, Tim Reddy, Rami Rauch, Chris Partridge. Illumina gene expression group: Gary Schroth, Shujun Luo, Eric Vermaas. TopHat/Cufflinks development: Cole Trapnell, Lior Pachter, Steven Salzberg. Contacts: Georgi Marinov (data coordination/informatics/experimental), Diane Trout (informatics) and Brian Williams (experimental). References Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeRnaSeqSuper ENC RNA-seq ENCODE RNA-seq Expression Description RNA sequencing, or RNA-seq, is a method for mapping and quantifying the total amount of RNA transcripts in a cell at any given time, otherwise known as the transcriptome, for any organism that has a genomic DNA sequence assembly. Compared to microarrays that detect and quantify transcripts by hybridization against known sequences, RNA-seq directly sequences transcripts and is especially well-suited for de novo discovery of RNA splicing patterns and for determining unequivocally the presence or absence of lower abundance class RNAs. RNA-seq is performed by reverse-transcribing an RNA sample into cDNA followed by high throughput DNA sequencing. Most data is produced in the format of either single reads or paired-end reads. In the format of single reads each sequence read comes from one end of a randomly primed cDNA molecule (and represent one end of one cDNA segment), while paired-end reads are obtained as pairs from both ends of a randomly primed cDNA (and represent two opposite ends of one cDNA segment). The resulting sequence reads are then informatically mapped onto the genome sequence (Alignments). The current mappers (TopHat and STAR) have the ability to map reads to annotated and unannotated genomic regions. Reads mapped to annotated or novel RNA splice junctions are (Splice Sites). Earlier versions of this software did not map reads to unannotated genomic regions. Some RNA-seq protocols do not specify the coding strand. As a result, there can be ambiguity at loci where both strands are transcribed. Display Conventions These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annual Review of Genomics and Human Genetics. 2009;10:135-51. Metzker ML. Sequencing technologies - the next generation. Nature Reviews: Genetics. 2010 Jan;11(1):31-46 Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeCaltechRnaSeqViewSplices Splice Juctions RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Il200SplicesRep2V2 NHLF 2x75 Sp 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001422 1422 GSM958746 Myers Caltech 11588 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Il200SplicesRep2V2 Splices lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHLF 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Il200SplicesRep1V2 NHLF 2x75 Sp 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001422 1422 GSM958746 Myers Caltech 11587 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Il200SplicesRep1V2 Splices lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHLF 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR1x75dSplicesRep1V2 NHEK 1x75D Sp 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000136 136 GSM958741 Myers Caltech 11204 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqNhekR1x75dSplicesRep1V2 Splices epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHEK single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Il200SplicesRep2V2 NHEK 2x75 Sp 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000131 131 GSM958736 Myers Caltech 11586 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhekR2x75Il200SplicesRep2V2 Splices epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHEK 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Il200SplicesRep1V2 NHEK 2x75 Sp 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000131 131 GSM958736 Myers Caltech 10884 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhekR2x75Il200SplicesRep1V2 Splices epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions NHEK 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Il200SplicesRep2V2 HSMM 2x75 Sp 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001420 1420 GSM958744 Myers Caltech 11585 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Il200SplicesRep2V2 Splices skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HSMM 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Il200SplicesRep1V2 HSMM 2x75 Sp 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001420 1420 GSM958744 Myers Caltech 11584 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Il200SplicesRep1V2 Splices skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HSMM 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep2V2 HCT6 2x75 Sp 2 HCT-116 RnaSeq ENCODE Mar 2012 Freeze 2011-02-12 2011-11-11 wgEncodeEH001425 1425 GSM958749 Myers Caltech 12097 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep2V2 Splices colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HCT-116 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep1V2 HCT6 2x75 Sp 1 HCT-116 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001425 1425 GSM958749 Myers Caltech 12096 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Il200SplicesRep1V2 Splices colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HCT-116 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep3V2 GM92 2x75 Sp 3 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 GSM958748 Myers Caltech SL2973 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep3V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12892 200 bp paired read RNA-seq Splices Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep2V2 GM92 2x75 Sp 2 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 GSM958748 Myers Caltech SL2970 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12892 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep1V2 GM92 2x75 Sp 1 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 GSM958748 Myers Caltech 11039 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200SplicesRep1V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12892 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Il200SplicesRep2V2 GM91 2x75 Sp 2 GM12891 RnaSeq ENCODE Mar 2012 Freeze 2011-03-14 2011-12-14 wgEncodeEH001423 1423 GSM958747 Myers Caltech SL2971 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Il200SplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12891 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Il200SplicesRep1V2 GM91 2x75 Sp 1 GM12891 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001423 1423 GSM958747 Myers Caltech 11038 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Il200SplicesRep1V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12891 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep3V2 MCF7 2x75 Sp 3 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2011-04-20 2012-01-20 wgEncodeEH001421 1421 GSM958745 Myers Caltech 12098 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep3V2 Splices mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions MCF-7 200 bp paired read RNA-seq Splices Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep2V2 MCF7 2x75 Sp 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001421 1421 GSM958745 Myers Caltech 11582 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep2V2 Splices mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions MCF-7 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep1V2 MCF7 2x75 Sp 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2011-01-22 2011-10-21 wgEncodeEH001421 1421 GSM958745 Myers Caltech 11581 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200SplicesRep1V2 Splices mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions MCF-7 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Il200Myc7dSplicesRep1 LHCND 2x75 Sp 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-05 2012-02-05 wgEncodeEH001670 1670 GSM958751 Myers Caltech 11622 myocyte cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Il200Myc7dSplicesRep1 DIFF_7d Splices skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Myocytes differentiated from myoblasts for 7 days. See specific cell protocol for treatment details. (Wold) Subset of aligned reads that cross splice junctions LHCN-M2 Myocyte 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Il200SplicesRep1V2 LHCN 2x75 Sp 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEH001669 1669 GSM958750 Myers Caltech 11621 myoblast cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Il200SplicesRep1V2 Splices skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions LHCN-M2 Myoblast 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dSplicesRep2V2 HUVEC 1x75D Sp 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000133 133 GSM958738 Myers Caltech 11205 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHuvecR1x75dSplicesRep2V2 Splices umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HUVEC single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dSplicesRep1V2 HUVEC 1x75D Sp 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000133 133 GSM958738 Myers Caltech 11206 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHuvecR1x75dSplicesRep1V2 Splices umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HUVEC single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Il200SplicesRep2V2 HUVEC 2x75 Sp 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000129 129 GSM958734 Myers Caltech 10885 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Il200SplicesRep2V2 Splices umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HUVEC 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Il200SplicesRep1V2 HUVEC 2x75 Sp 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000129 129 GSM958734 Myers Caltech 10883 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Il200SplicesRep1V2 Splices umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HUVEC 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dSplicesRep2V2 HepG 1x75D Sp 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000135 135 GSM958740 Myers Caltech 11209 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHepg2R1x75dSplicesRep2V2 Splices hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HepG2 single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dSplicesRep1V2 HepG 1x75D Sp 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000135 135 GSM958740 Myers Caltech 11210 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHepg2R1x75dSplicesRep1V2 Splices hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HepG2 single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Il200SplicesRep2V2 HepG 2x75 Sp 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-22 2010-10-22 wgEncodeEH000127 127 GSM958732 Myers Caltech 10879 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Il200SplicesRep2V2 Splices hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HepG2 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Il200SplicesRep1V2 HepG 2x75 Sp 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-12 2010-10-11 wgEncodeEH000127 127 GSM958732 Myers Caltech 10878 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Il200SplicesRep1V2 Splices hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HepG2 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dSplicesRep2V2 HeLa 1x75D Sp 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000134 134 GSM958739 Myers Caltech 11207 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHelas3R1x75dSplicesRep2V2 Splices cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HeLa-S3 single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dSplicesRep1V2 HeLa 1x75D Sp 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000134 134 GSM958739 Myers Caltech 11208 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHelas3R1x75dSplicesRep1V2 Splices cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HeLa-S3 single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Il200SplicesRep2V2 HeLa 2x75 Sp 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 GSM958735 Myers Caltech 10882 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Il200SplicesRep2V2 Splices cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HeLa-S3 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Il200SplicesRep1V2 HeLa 2x75 Sp 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 GSM958735 Myers Caltech 10881 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Il200SplicesRep1V2 Splices cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions HeLa-S3 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dSplicesRep2V2 K562 1x75D Sp 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-06 2010-10-06 wgEncodeEH000126 126 GSM958731 Myers Caltech 11007 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqK562R1x75dSplicesRep2V2 Splices leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions K562 single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dSplicesRep1V2 K562 1x75D Sp 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-06 2010-10-06 wgEncodeEH000126 126 GSM958731 Myers Caltech 11008 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqK562R1x75dSplicesRep1V2 Splices leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions K562 single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Il200SplicesRep2V2 K562 2x75 Sp 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000124 124 GSM958729 Myers Caltech 10567 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqK562R2x75Il200SplicesRep2V2 Splices leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions K562 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Il200SplicesRep1V2 K562 2x75 Sp 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000124 124 GSM958729 Myers Caltech 10517 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqK562R2x75Il200SplicesRep1V2 Splices leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions K562 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dSplicesRep2V2 H1ES 1x75D Sp 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000132 132 GSM958737 Myers Caltech 11009 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqH1hescR1x75dSplicesRep2V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dSplicesRep1V2 H1ES 1x75D Sp 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000132 132 GSM958737 Myers Caltech 10947 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqH1hescR1x75dSplicesRep1V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il400SplicesRep1V2 H1ES 400 Sp 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000138 138 GSM958743 Myers Caltech 10876 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il400SplicesRep1V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 400 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep4V2 H1ES 2x75 Sp 4 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000128 128 GSM958733 Myers Caltech 10874 cell TH1014 hg18 2x75 4 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep4V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 200 bp paired read RNA-seq Splices Rep 4 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep3V2 H1ES 2x75 Sp 3 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-13 wgEncodeEH000128 128 GSM958733 Myers Caltech 11289 cell TH1014 hg18 2x75 3 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep3V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 200 bp paired read RNA-seq Splices Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep2V2 H1ES 2x75 Sp 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-13 wgEncodeEH000128 128 GSM958733 Myers Caltech 11288 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep2V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep1V2 H1ES 2x75 Sp 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-13 wgEncodeEH000128 128 GSM958733 Myers Caltech 11286 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200SplicesRep1V2 Splices embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions H1-hESC 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep2V2 GM78 1x75D Sp 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-06 2010-10-06 wgEncodeEH000125 125 GSM958730 Myers Caltech 11010 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 single read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep1V2 GM78 1x75D Sp 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-04 2010-10-04 wgEncodeEH000125 125 GSM958730 Myers Caltech 11011 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep1V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 single read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il400SplicesRep2V2 GM78 400 Sp 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000137 137 GSM958742 Myers Caltech 10516 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il400SplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 400 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep2V2 GM78 2x75 Sp 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000122 122 GSM958728 Myers Caltech 10515 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep2V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 200 bp paired read RNA-seq Splices Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep1V2 GM78 2x75 Sp 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000122 122 GSM958728 Myers Caltech 10565 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep1V2 Splices B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Subset of aligned reads that cross splice junctions GM12878 200 bp paired read RNA-seq Splices Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqViewSignal Signal RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Th1014Il200SigRep2V4 NHLF 2x75 Sg 2 NHLF RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001422 1422 GSM958746 Myers Caltech 11588 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Th1014Il200SigRep2V4 Signal lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal NHLF 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Th1014Il200SigRep1V4 NHLF 2x75 Sg 1 NHLF RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001422 1422 GSM958746 Myers Caltech 11587 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Th1014Il200SigRep1V4 Signal lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal NHLF 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Th1014Il200USigRep2V4 NHEK 2x75 Sg 2 NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-03-26 2011-05-11 2012-02-11 wgEncodeEH000131 131 GSM958736 Myers Caltech 11586 cell TH1014 2x75 2 longPolyA U wgEncodeCaltechRnaSeqNhekR2x75Th1014Il200USigRep2V4 Signal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Unknown Signal NHEK 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Th1014Il200USigRep1V4 NHEK 2x75 Sg 1 NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-03-26 2011-05-11 2012-02-11 wgEncodeEH000131 131 GSM958736 Myers Caltech 10884 cell TH1014 2x75 1 longPolyA U wgEncodeCaltechRnaSeqNhekR2x75Th1014Il200USigRep1V4 Signal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Unknown Signal NHEK 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Th1014Il200SigRep2V4 HSMM 2x75 Sg 2 HSMM RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001420 1420 GSM958744 Myers Caltech 11585 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Th1014Il200SigRep2V4 Signal skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HSMM 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Th1014Il200SigRep1V4 HSMM 2x75 Sg 1 HSMM RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001420 1420 GSM958744 Myers Caltech 11584 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Th1014Il200SigRep1V4 Signal skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HSMM 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep2V4 HCT6 2x75 Sg 2 HCT-116 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001425 1425 GSM958749 Myers Caltech 12097 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep2V4 Signal colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HCT-116 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep1V4 HCT6 2x75 Sg 1 HCT-116 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001425 1425 GSM958749 Myers Caltech 12096 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Th1014Il200SigRep1V4 Signal colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HCT-116 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep3V4 GM92 2x75 Sg 3 GM12892 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001424 1424 GSM958748 Myers Caltech SL2973 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep3V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12892 200 bp paired read RNA-seq Signal Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep2V4 GM92 2x75 Sg 2 GM12892 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001424 1424 GSM958748 Myers Caltech SL2970 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep2V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12892 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep1V4 GM92 2x75 Sg 1 GM12892 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001424 1424 GSM958748 Myers Caltech 11039 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep1V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12892 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Th1014Il200SigRep2V4 GM91 2x75 Sg 2 GM12891 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001423 1423 GSM958747 Myers Caltech SL2971 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Th1014Il200SigRep2V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12891 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Th1014Il200SigRep1V4 GM91 2x75 Sg 1 GM12891 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001423 1423 GSM958747 Myers Caltech 11038 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Th1014Il200SigRep1V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12891 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep3V4 MCF7 2x75 Sg 3 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001421 1421 GSM958745 Myers Caltech 12098 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep3V4 Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal MCF-7 200 bp paired read RNA-seq Signal Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep2V4 MCF7 2x75 Sg 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001421 1421 GSM958745 Myers Caltech 11582 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep2V4 Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal MCF-7 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep1V4 MCF7 2x75 Sg 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH001421 1421 GSM958745 Myers Caltech 11581 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep1V4 Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal MCF-7 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Th1014Il200Diff7dSigRep1V4 LHCND 2x75 Sg 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-26 2011-05-11 2012-02-11 wgEncodeEH001670 1670 GSM958751 Myers Caltech 11622 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Th1014Il200Diff7dSigRep1V4 DIFF_7d Signal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Myocytes differentiated from myoblasts for 7 days. See specific cell protocol for treatment details. (Wold) Signal LHCN-M2 Myocyte 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Th1014Il200USigRep1V4 LHCN 2x75 Sg 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-26 2011-05-11 2012-02-11 wgEncodeEH001669 1669 GSM958750 Myers Caltech 11621 cell TH1014 2x75 1 longPolyA U wgEncodeCaltechRnaSeqLhcnm2R2x75Th1014Il200USigRep1V4 Signal skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Unknown Signal LHCN-M2 Myoblast 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Th1014Il200SigRep2V4 HUVEC 2x75 Sg 2 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000129 129 GSM958734 Myers Caltech 10885 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Th1014Il200SigRep2V4 Signal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HUVEC 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Th1014Il200SigRep1V4 HUVEC 2x75 Sg 1 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000129 129 GSM958734 Myers Caltech 10883 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Th1014Il200SigRep1V4 Signal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HUVEC 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Th1014Il200SigRep2V4 HepG 2x75 Sg 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000127 127 GSM958732 Myers Caltech 10879 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Th1014Il200SigRep2V4 Signal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HepG2 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Th1014Il200SigRep1V4 HepG 2x75 Sg 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000127 127 GSM958732 Myers Caltech 10878 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Th1014Il200SigRep1V4 Signal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HepG2 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Th1014Il200SigRep2V4 HeLa 2x75 Sg 2 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000130 130 GSM958735 Myers Caltech 10882 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Th1014Il200SigRep2V4 Signal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HeLa-S3 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Th1014Il200SigRep1V4 HeLa 2x75 Sg 1 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000130 130 GSM958735 Myers Caltech 10881 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Th1014Il200SigRep1V4 Signal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal HeLa-S3 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Th1014Il200SigRep2V4 K562 2x75 Sg 2 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000124 124 GSM958729 Myers Caltech 10567 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqK562R2x75Th1014Il200SigRep2V4 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal K562 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Th1014Il200SigRep1V4 K562 2x75 Sg 1 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000124 124 GSM958729 Myers Caltech 10517 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqK562R2x75Th1014Il200SigRep1V4 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal K562 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il400SigRep1V4 H1ES 400 Sg 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000138 138 GSM958743 Myers Caltech 10876 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il400SigRep1V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 400 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep4V4 H1ES 2x75 Sg 4 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000128 128 GSM958733 Myers Caltech 10874 cell TH1014 2x75 4 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep4V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 200 bp paired read RNA-seq Signal Rep 4 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep3V4 H1ES 2x75 Sg 3 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000128 128 GSM958733 Myers Caltech 11289 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep3V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 200 bp paired read RNA-seq Signal Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep2V4 H1ES 2x75 Sg 2 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000128 128 GSM958733 Myers Caltech 11288 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep2V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep1V4 H1ES 2x75 Sg 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000128 128 GSM958733 Myers Caltech 11286 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Th1014Il200SigRep1V4 Signal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal H1-hESC 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il400USigRep2V4 GM78 400 Sg 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000137 137 GSM958742 Myers Caltech 10516 cell TH1014 2x75 2 longPolyA U wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il400USigRep2V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Unknown Signal GM12878 400 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep2V4 GM78 2x75 Sg 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000122 122 GSM958728 Myers Caltech 10515 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep2V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12878 200 bp paired read RNA-seq Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep1V4 GM78 2x75 Sg 1 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2011-05-11 2012-02-11 wgEncodeEH000122 122 GSM958728 Myers Caltech 10565 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep1V4 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Signal GM12878 200 bp paired read RNA-seq Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqViewPlusSignal Plus Raw Signal RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR1x75dTh1014UPlusRawRep1V4 NHEK 1x75D + 1 NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000136 136 GSM958741 Myers Caltech 11204 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqNhekR1x75dTh1014UPlusRawRep1V4 PlusRawSignal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand NHEK single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UPlusRawRep2V4 HUVEC 1x75D + 2 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000133 133 GSM958738 Myers Caltech 11205 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UPlusRawRep2V4 PlusRawSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HUVEC single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UPlusRawRep1V4 HUVEC 1x75D + 1 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000133 133 GSM958738 Myers Caltech 11206 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UPlusRawRep1V4 PlusRawSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HUVEC single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UPlusRawRep2V4 HepG 1x75D + 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000135 135 GSM958740 Myers Caltech 11209 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UPlusRawRep2V4 PlusRawSignal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HepG2 single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UPlusRawRep1V4 HepG 1x75D + 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000135 135 GSM958740 Myers Caltech 11210 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UPlusRawRep1V4 PlusRawSignal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HepG2 single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UPlusRawRep2V4 HeLa 1x75D + 2 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000134 134 GSM958739 Myers Caltech 11207 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UPlusRawRep2V4 PlusRawSignal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HeLa-S3 single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UPlusRawRep1V4 HeLa 1x75D + 1 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000134 134 GSM958739 Myers Caltech 11208 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UPlusRawRep1V4 PlusRawSignal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand HeLa-S3 single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dTh1014UPlusRawRep2V4 K562 1x75D + 2 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000126 126 GSM958731 Myers Caltech 11007 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqK562R1x75dTh1014UPlusRawRep2V4 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand K562 single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dTh1014UPlusRawRep1V4 K562 1x75D + 1 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000126 126 GSM958731 Myers Caltech 11008 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqK562R1x75dTh1014UPlusRawRep1V4 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand K562 single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UPlusRawRep2V4 H1ES 1x75D + 2 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000132 132 GSM958737 Myers Caltech 11009 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UPlusRawRep2V4 PlusRawSignal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand H1-hESC single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UPlusRawRep1V4 H1ES 1x75D + 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000132 132 GSM958737 Myers Caltech 10947 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UPlusRawRep1V4 PlusRawSignal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand H1-hESC single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UPlusRawRep2V4 GM78 1x75D + 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000125 125 GSM958730 Myers Caltech 11010 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UPlusRawRep2V4 PlusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand GM12878 single read RNA-seq Plus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UPlusRawRep1V4 GM78 1x75D + 1 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000125 125 GSM958730 Myers Caltech 11011 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UPlusRawRep1V4 PlusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the plus strand GM12878 single read RNA-seq Plus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqViewMinusSignal Minus Raw Signal RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR1x75dTh1014UMinusRawRep1V4 NHEK 1x75D - 1 NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000136 136 GSM958741 Myers Caltech 11204 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqNhekR1x75dTh1014UMinusRawRep1V4 MinusRawSignal epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand NHEK single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UMinusRawRep2V4 HUVEC 1x75D - 2 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000133 133 GSM958738 Myers Caltech 11205 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UMinusRawRep2V4 MinusRawSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HUVEC single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UMinusRawRep1V4 HUVEC 1x75D - 1 HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000133 133 GSM958738 Myers Caltech 11206 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHuvecR1x75dTh1014UMinusRawRep1V4 MinusRawSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HUVEC single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UMinusRawRep2V4 HepG 1x75D - 2 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000135 135 GSM958740 Myers Caltech 11209 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UMinusRawRep2V4 MinusRawSignal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HepG2 single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UMinusRawRep1V4 HepG 1x75D - 1 HepG2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000135 135 GSM958740 Myers Caltech 11210 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHepg2R1x75dTh1014UMinusRawRep1V4 MinusRawSignal hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HepG2 single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UMinusRawRep2V4 HeLa 1x75D - 2 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000134 134 GSM958739 Myers Caltech 11207 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UMinusRawRep2V4 MinusRawSignal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HeLa-S3 single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UMinusRawRep1V4 HeLa 1x75D - 1 HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000134 134 GSM958739 Myers Caltech 11208 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqHelas3R1x75dTh1014UMinusRawRep1V4 MinusRawSignal cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand HeLa-S3 single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dTh1014UMinusRawRep2V4 K562 1x75D - 2 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000126 126 GSM958731 Myers Caltech 11007 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqK562R1x75dTh1014UMinusRawRep2V4 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand K562 single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dTh1014UMinusRawRep1V4 K562 1x75D - 1 K562 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000126 126 GSM958731 Myers Caltech 11008 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqK562R1x75dTh1014UMinusRawRep1V4 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand K562 single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UMinusRawRep2V4 H1ES 1x75D - 2 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000132 132 GSM958737 Myers Caltech 11009 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UMinusRawRep2V4 MinusRawSignal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand H1-hESC single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UMinusRawRep1V4 H1ES 1x75D - 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000132 132 GSM958737 Myers Caltech 10947 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqH1hescR1x75dTh1014UMinusRawRep1V4 MinusRawSignal embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand H1-hESC single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UMinusRawRep2V4 GM78 1x75D - 2 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000125 125 GSM958730 Myers Caltech 11010 cell TH1014 1x75D 2 longPolyA U wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UMinusRawRep2V4 MinusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand GM12878 single read RNA-seq Minus Signal Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UMinusRawRep1V4 GM78 1x75D - 1 GM12878 RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2011-05-11 2012-02-11 wgEncodeEH000125 125 GSM958730 Myers Caltech 11011 cell TH1014 1x75D 1 longPolyA U wgEncodeCaltechRnaSeqGm12878R1x75dTh1014UMinusRawRep1V4 MinusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Unknown Graphs the base-by-base density of tags on the minus strand GM12878 single read RNA-seq Minus Signal Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqViewAligns Alignments RNA-seq from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Il200AlignsRep2V2 NHLF 2x75 A 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001422 1422 Myers Caltech 11588 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Il200AlignsRep2V2 Alignments lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhlfR2x75Il200AlignsRep1V2 NHLF 2x75 A 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001422 1422 Myers Caltech 11587 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhlfR2x75Il200AlignsRep1V2 Alignments lung fibroblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR1x75dAlignsRep1V2 NHEK 1x75D A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000136 136 Myers Caltech 11204 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqNhekR1x75dAlignsRep1V2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Il200AlignsRep2V2 NHEK 2x75 A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000131 131 Myers Caltech 11586 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqNhekR2x75Il200AlignsRep2V2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqNhekR2x75Il200AlignsRep1V2 NHEK 2x75 A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000131 131 Myers Caltech 10884 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqNhekR2x75Il200AlignsRep1V2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Il200AlignsRep2V2 HSMM 2x75 A 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001420 1420 Myers Caltech 11585 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Il200AlignsRep2V2 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHsmmR2x75Il200AlignsRep1V2 HSMM 2x75 A 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001420 1420 Myers Caltech 11584 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHsmmR2x75Il200AlignsRep1V2 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Il200AlignsRep2V2 HCT6 2x75 A 2 HCT-116 RnaSeq ENCODE Mar 2012 Freeze 2011-02-12 2011-11-11 wgEncodeEH001425 1425 Myers Caltech 12097 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Il200AlignsRep2V2 Alignments colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HCT-116 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHct116R2x75Il200AlignsRep1V2 HCT6 2x75 A 1 HCT-116 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001425 1425 Myers Caltech 12096 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqHct116R2x75Il200AlignsRep1V2 Alignments colorectal carcinoma (PMID: 7214343) Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HCT-116 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep3V2 GM92 2x75 A 3 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 Myers Caltech SL2973 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep3V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12892 200 bp paired read RNA-seq Alignments Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep2V2 GM92 2x75 A 2 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 Myers Caltech SL2970 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12892 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep1V2 GM92 2x75 A 1 GM12892 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001424 1424 Myers Caltech 11039 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12892R2x75Il200AlignsRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12892 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Il200AlignsRep2V2 GM91 2x75 A 2 GM12891 RnaSeq ENCODE Mar 2012 Freeze 2011-03-14 2011-12-14 wgEncodeEH001423 1423 Myers Caltech SL2971 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Il200AlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12891 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12891R2x75Il200AlignsRep1V2 GM91 2x75 A 1 GM12891 RnaSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001423 1423 Myers Caltech 11038 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12891R2x75Il200AlignsRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12891 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep3V2 MCF7 2x75 A 3 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2011-02-12 2011-11-11 wgEncodeEH001421 1421 Myers Caltech 12098 cell TH1014 2x75 3 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep3V2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 200 bp paired read RNA-seq Alignments Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep2V2 MCF7 2x75 A 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001421 1421 Myers Caltech 11582 cell TH1014 2x75 2 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep2V2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep1V2 MCF7 2x75 A 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2011-01-22 2011-10-21 wgEncodeEH001421 1421 Myers Caltech 11581 cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqMcf7R2x75Il200AlignsRep1V2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Il200Myc7dAlignsRep1 LHCND 2x75 A 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2011-05-05 2012-02-05 wgEncodeEH001670 1670 Myers Caltech 11622 myocyte cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Il200Myc7dAlignsRep1 DIFF_7d Alignments skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Myocytes differentiated from myoblasts for 7 days. See specific cell protocol for treatment details. (Wold) Shows individual reads mapped to the genome and indicates where bases may mismatch LHCN-M2 Myocyte 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqLhcnm2R2x75Il200AlignsRep1V2 LHCN 2x75 A 1 LHCN-M2 RnaSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEH001669 1669 Myers Caltech 11621 myoblast cell TH1014 2x75 1 longPolyA wgEncodeCaltechRnaSeqLhcnm2R2x75Il200AlignsRep1V2 Alignments skeletal myoblasts derived from satellite cells from the pectoralis major muscle of a 41 year old caucasian heart transplant donor, immortalized with lox-hygro-hTERT ("LH"), and Cdk4-neo ("CN"), Zhu et al. (2007) in Aging Cell, vol. 6, pp 515-523, newly promoted to tier 2: not in 2011 analysis. Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch LHCN-M2 Myoblast 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dAlignsRep2V2 HUVEC 1x75D A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000133 133 Myers Caltech 11205 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHuvecR1x75dAlignsRep2V2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR1x75dAlignsRep1V2 HUVEC 1x75D A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000133 133 Myers Caltech 11206 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHuvecR1x75dAlignsRep1V2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Il200AlignsRep2V2 HUVEC 2x75 A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000129 129 Myers Caltech 10885 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Il200AlignsRep2V2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHuvecR2x75Il200AlignsRep1V2 HUVEC 2x75 A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000129 129 Myers Caltech 10883 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHuvecR2x75Il200AlignsRep1V2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dAlignsRep2V3 HepG 1x75D A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-09-08 2010-01-14 2010-10-14 wgEncodeEH000135 135 Myers Caltech 11209 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHepg2R1x75dAlignsRep2V3 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R1x75dAlignsRep1V3 HepG 1x75D A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-09-08 2010-01-14 2010-10-14 wgEncodeEH000135 135 Myers Caltech 11210 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHepg2R1x75dAlignsRep1V3 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Il200AlignsRep2V2 HepG 2x75 A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-22 2010-10-22 wgEncodeEH000127 127 Myers Caltech 10879 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Il200AlignsRep2V2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHepg2R2x75Il200AlignsRep1V2 HepG 2x75 A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-12 2010-10-11 wgEncodeEH000127 127 Myers Caltech 10878 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHepg2R2x75Il200AlignsRep1V2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dAlignsRep2V2 HeLa 1x75D A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000134 134 Myers Caltech 11207 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqHelas3R1x75dAlignsRep2V2 Alignments cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R1x75dAlignsRep1V2 HeLa 1x75D A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000134 134 Myers Caltech 11208 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqHelas3R1x75dAlignsRep1V2 Alignments cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Il200AlignsRep2V2 HeLa 2x75 A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 Myers Caltech 10882 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Il200AlignsRep2V2 Alignments cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqHelas3R2x75Il200AlignsRep1V2 HeLa 2x75 A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-12 wgEncodeEH000130 130 Myers Caltech 10881 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqHelas3R2x75Il200AlignsRep1V2 Alignments cervical carcinoma Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dAlignsRep2V2 K562 1x75D A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-06 2010-10-06 wgEncodeEH000126 126 Myers Caltech 11007 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqK562R1x75dAlignsRep2V2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R1x75dAlignsRep1V2 K562 1x75D A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-06 2010-10-06 wgEncodeEH000126 126 Myers Caltech 11008 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqK562R1x75dAlignsRep1V2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Il200AlignsRep2V2 K562 2x75 A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000124 124 Myers Caltech 10567 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqK562R2x75Il200AlignsRep2V2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqK562R2x75Il200AlignsRep1V2 K562 2x75 A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000124 124 Myers Caltech 10517 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqK562R2x75Il200AlignsRep1V2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dAlignsRep2V2 H1ES 1x75D A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2010-01-14 2010-10-14 wgEncodeEH000132 132 Myers Caltech 11009 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqH1hescR1x75dAlignsRep2V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR1x75dAlignsRep1V2 H1ES 1x75D A 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-14 wgEncodeEH000132 132 Myers Caltech 10947 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqH1hescR1x75dAlignsRep1V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il400AlignsRep1V2 H1ES 400 A 1 H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000138 138 Myers Caltech 10876 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il400AlignsRep1V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 400 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep4V2 H1ES 2x75 A 4 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000128 128 Myers Caltech 10874 cell TH1014 hg18 2x75 4 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep4V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 200 bp paired read RNA-seq Alignments Rep 4 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep3V2 H1ES 2x75 A 3 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-13 wgEncodeEH000128 128 Myers Caltech 11289 cell TH1014 hg18 2x75 3 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep3V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 200 bp paired read RNA-seq Alignments Rep 3 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep2V2 H1ES 2x75 A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-14 2010-10-13 wgEncodeEH000128 128 Myers Caltech 11288 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep2V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep1V2 H1ES 2x75 A 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-13 2010-10-13 wgEncodeEH000128 128 Myers Caltech 11286 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep1V2 Alignments embryonic stem cells Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2 GM78 1x75D A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-06 2010-10-06 wgEncodeEH000125 125 Myers Caltech 11010 cell TH1014 hg18 1x75D 2 longPolyA wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 single read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep1V2 GM78 1x75D A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-04 2010-10-04 wgEncodeEH000125 125 Myers Caltech 11011 cell TH1014 hg18 1x75D 1 longPolyA wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Single 75 nt directed reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 single read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il400AlignsRep2V2 GM78 400 A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2010-01-15 2010-10-14 wgEncodeEH000137 137 Myers Caltech 10516 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il400AlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 400 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il200AlignsRep2V2 GM78 2x75 A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000122 122 Myers Caltech 10515 cell TH1014 hg18 2x75 2 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il200AlignsRep2V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 200 bp paired read RNA-seq Alignments Rep 2 from ENCODE/Caltech Expression 
wgEncodeCaltechRnaSeqGm12878R2x75Il200AlignsRep1V2 GM78 2x75 A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2009-03-06 2009-12-06 wgEncodeEH000122 122 Myers Caltech 10565 cell TH1014 hg18 2x75 1 longPolyA wgEncodeCaltechRnaSeqGm12878R2x75Il200AlignsRep1V2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Myers Wold - California Institute of Technology Whole cell TopHat v1.0.14 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 200 bp paired read RNA-seq Alignments Rep 1 from ENCODE/Caltech Expression 
wgEncodeCshlLongRnaSeq CSHL Long RNA-seq GSE30567 Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression Description These tracks were generated by the ENCODE Consortium. They contain information about human RNAs greater than 200 nucleotides in length that were obtained as short reads from the Illumina GAIIx platform. Data are available from biological replicates of several cell lines. In addition to profiling Poly-A+ and Poly-A- RNA from whole cells, there are also data from various subcellular compartments. In many cases, there are Cap Analysis of Gene Expression (CAGE, see the RIKEN CAGE Loc track), Small RNA-seq (less than 200 nucleotides, see the CSHL Sm RNA-seq track) and Pair-End di-TAG-RNA (PET-RNA, see the GIS RNA PET track) datasets available from the same biological replicates. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Color differences among the views are arbitrary. They provide a visual cue for distinguishing between the different cell types and compartments. Contigs The Contigs represent blocks of overlapping mapped reads from the pooled biological replicates. Specific column specifications can be found in the supplemental directory. Signals The Plus Signal and Minus Signal views show the density of mapped reads on the plus and minus strands (wiggle format), respectively. Alignments The Alignments view shows individual reads mapped from biological replicates to the genome and indicates where bases may mismatch. Every mapped read is displayed, i.e. uncollapsed. The alignment file follows the standard SAM format. See the SAM Format Specification for more information on the SAM/BAM file format. Splice Junctions Subset of aligned reads that cross splice junctions. Specific column specifications can be found in the supplemental directory. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Additional views are available on the downloads page. Methods Cell Culture Cells were grown according to the approved ENCODE cell culture protocols. Library Preparation The published cDNA sequencing protocol was used. This protocol generates directional libraries and reports the transcripts' strand of origin. Exogenous RNA spike-ins were added to each endogenous RNA isolate and carried through library construction and sequencing. The Illumina PhiX control library was also spiked-in at 1% to each completed human library just prior to cluster formation. Accompanying each RNA-seq dataset is a Protocol document available for download as a PDF. This document contains details about the RNA isolations and treatments, library construction, spike-ins as well as quality control figures for individual libraries. The spike-in sequence and the concentrations are available for download in the supplemental directory. Sequencing and Mapping The libraries were sequenced on the Illumina GAIIx platform as paired-ends for 76 or 101 cycles for each read. The average depth of sequencing was ~200 million reads (100 million paired-ends). The data were mapped against hg19 using Spliced Transcript Alignment and Reconstruction (STAR) written by Alex Dobin (CSHL). More information about STAR, including the parameters used for these data, is available from the Gingeras lab. For each experiment there are additional element data views data files available for download. These elements were assessed for reproducibility using a nonparametric irreproducible detection (IDR) rate script. The IDR values for each element are included in the files for end-users to use as a threshold. An IDR value of 0.1 means that the probability of detecting that element in a third experiment equivalent in depth to the sum of the bioreplicates is 90%. In addition, expression values for annotated genes, transcripts and exons were computed. Further explanation of these files is available for download in the supplemental directory. Verification FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated for annotated Gencode exons and Spearman values were compared. In general, Rho values are greater than .90 between biological replicates. Release Notes This is release 3 (Sept 2012) of this track for hg19. It has no new experiments, but has additional files for many experiments. The hMNC-CB experiment has been revoked. The doubly compressed spike-ins files have been uncompressed. The hMNC-PB experiment has been replaced with improved depth. The current downloadable elements files (Transcripts, Genes and Exons) were generated using GENCODE V10, while the older datasets were generated using GENCODE V7. The "view" metadata will specify V7 or V10 for these files. Errata 6/6/2013 - CSHL reports that one lane of reads is missing from the SK-N-SH-RA fastq read2 file (wgEncodeCshlLongRnaSeqSknshraCellPapFastqRd2Rep1.fastq.gz). Credits These data were generated and analyzed by the transcriptome group led by Tom Gingeras at Cold Spring Harbor Laboratories and the laboratory of Roderic Guigo at the Center for Genomic Regulation (CRG) in Barcelona. Contact: Carrie Davis References Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Oct;37(18):e123. Publications Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y et al. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res. 2012 Sep;22(9):1658-67. Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR et al. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet. 2011 Oct 23;43(12):1179-85. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res. 2012 Sep;22(9):1775-89. Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E et al. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol. 2012 Sep 5;13(9):R53. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 2011 Sep;21(9):1543-51. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeCshlLongRnaSeqViewJunctions Splice Junctions Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapJunctions SKRA cel pA+ J SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967,LID8968 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapJunctions Junctions neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH RA whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPamJunctions SKRA cel pA- J SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003,LID9011 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPamJunctions Junctions neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH RA whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmcCellTotalJunctions SkMC cel tot J SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47245,LID47246 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmcCellTotalJunctions Junctions Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SkMC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapJunctions NHLF cel pA+ J NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692,LID8701 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapJunctions Junctions lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHLF whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPamJunctions NHLF cel pA- J NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828,LID8829 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPamJunctions Junctions lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHLF whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm2CellTotalJunctions NHMM2 cel tot J NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47258,LID47259 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm2CellTotalJunctions Junctions Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEM M2 whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm2CellTotalJunctions NHMf cel tot J NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47256,LID47257 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm2CellTotalJunctions Junctions Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEM.f M2 whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapJunctions NHEK nuc pA+ J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797,LID8798 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPamJunctions NHEK nuc pA- J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204,LID9205 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPamJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapJunctions NHEK cyt pA+ J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795,LID8796 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPamJunctions NHEK cyt pA- J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPamJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapJunctions NHEK cel pA+ J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID8694 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPamJunctions NHEK cel pA- J NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8830 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPamJunctions Junctions epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHEK whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdfCellTotalJunctions NHDF cel tot J NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47247,LID47248 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdfCellTotalJunctions Junctions Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions NHDF whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwpCellTotalJunctions HWP cel tot J HWP RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47254,LID47255 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwpCellTotalJunctions Junctions Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HWP whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmfCellTotalJunctions HVMF cel tot J HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47249,LID47250 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmfCellTotalJunctions Junctions villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HVMF whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapJunctions HSMM cel pA+ J HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710,LID8711 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapJunctions Junctions skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HSMM whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPamJunctions HSMM cel pA- J HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826,LID8827 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPamJunctions Junctions skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HSMM whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalJunctions HSVEC cel tot J HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47261,LID47260 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalJunctions Junctions Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HSaVEC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalJunctions HPIEC cel tot J HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47105,LID47253 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalJunctions Junctions Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HPIEpC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalJunctions HPCPL cel tot J HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47301,LID47104 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalJunctions Junctions Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HPC-PL whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHobCellTotalJunctions HOB cel tot J HOB RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47251,LID47252 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHobCellTotalJunctions Junctions Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HOB whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscucCellTotalJunctions hMSUC cel tot J hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47299,LID47300 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscucCellTotalJunctions Junctions Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions hMSC-UC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbmCellTotalJunctions hMSBM cel tot J hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47099,LID47100 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbmCellTotalJunctions Junctions Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions hMSC-BM whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscatCellTotalJunctions hMSAT cel tot J hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47097,LID47098 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscatCellTotalJunctions Junctions Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions hMSC-AT whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalJunctionsV2 hMNPB cel tot J hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-07-04 2013-04-04 wgEncodeEH002878 2878 GSM984606 Gingeras CSHL LID47807 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalJunctionsV2 Junctions Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions hMNC-PB whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalJunctions HMEpC cel tot J HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002683 2683 GSM984621 Gingeras CSHL LID47096 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalJunctions Junctions Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HMEpC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapJunctions HMEC cel pA+ J HMEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapJunctions Junctions mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HMEC whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPamJunctions HMEC cel pA- J HMEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPamJunctions Junctions mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HMEC whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpcCellTotalJunctions HFDPC cel tot J HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47094,LID47095 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpcCellTotalJunctions Junctions Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HFDPC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHchCellTotalJunctions HCH cel tot J HCH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47024,LID47025 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHchCellTotalJunctions Junctions Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HCH whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalJunctions HAoEC cel tot J HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47022,LID47023 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalJunctions Junctions Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HAoEC whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalJunctions HAoAF cel tot J HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47021,LID47020 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalJunctions Junctions Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HAoAF whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalJunctions CD34 cel tot J CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-03-27 2012-12-27 wgEncodeEH002670 2670 GSM981257 Gingeras CSHL LID45901 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalJunctions Junctions hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions CD34+ Mobilized whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapJunctions BJ cel pA+ J BJ RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969,LID8970 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapJunctions Junctions skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions BJ whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPamJunctions BJ cel pA- J BJ RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007,LID9008 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPamJunctions Junctions skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions BJ whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapJunctions AG50 cel pA+ J AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965,LID8966 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapJunctions Junctions fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions AG04450 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPamJunctions AG50 cel pA- J AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001,LID9002 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPamJunctions Junctions fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions AG04450 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapJunctions SKNSH nuc pA+ J SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46596,LID46597 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapJunctions Junctions neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapJunctions SKNSH cyt pA+ J SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46594,LID46595 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapJunctions Junctions neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapJunctions SKNSH cel pA+ J SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46598,LID46599 iIDR cell 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapJunctions Junctions neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions SK-N-SH whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapJunctions CD14 cel pA+ J Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44594,LID44497 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapJunctions Junctions Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MonocytesCD14+ whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamJunctions CD14 cel pA- J Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44657,LID44658 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamJunctions Junctions Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MonocytesCD14+ whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapJunctions MCF7 nuc pA+ J MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46859,LID46860 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapJunctions Junctions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MCF-7 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapJunctions MCF7 cyt pA+ J MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46857,LID46858 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapJunctions Junctions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MCF-7 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapJunctions MCF7 cel pA+ J MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686,LID8687 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapJunctions Junctions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MCF-7 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPamJunctions MCF7 cel pA- J MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824,LID8825 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPamJunctions Junctions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions MCF-7 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapJunctions IMR90 nuc pA+ J IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45635,LID45613 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapJunctions Junctions fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions IMR90 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapJunctions IMR90 cyt pA+ J IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45611,LID45612 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapJunctions Junctions fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions IMR90 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalJunctions IMR90 cel tot J IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45238,LID45239 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalJunctions Junctions fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions IMR90 whole cell total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapJunctions IMR90 cel pA+ J IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45016,LID45017 iIDR cell 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapJunctions Junctions fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions IMR90 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapJunctions HUVEC nuc pA+ J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690,LID8691 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPamJunctions HUVEC nuc pA- J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206,LID9207 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPamJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapJunctions HUVEC cyt pA+ J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688,LID8689 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPamJunctions HUVEC cyt pA- J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPamJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapJunctions HUVEC cel pA+ J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463,LID8464 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPamJunctions HUVEC cel pA- J HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788,LID8789 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPamJunctions Junctions umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HUVEC whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapJunctions HeG2 nuc pA+ J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534,LID8535 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPamJunctions HeG2 nuc pA- J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202,LID9203 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPamJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapJunctions HeG2 cyt pA+ J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471,LID8472 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPamJunctions HeG2 cyt pA- J HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552,LID18553 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPamJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapJunctions HeG2 cel pA+ J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635,LID16636 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPamJunctions HeG2 cel pA- J HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792,LID8793 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPamJunctions Junctions hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HepG2 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapJunctions HeS3 nuc pA+ J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559,LID8560 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPamJunctions HeS3 nuc pA- J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200,LID9201 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPamJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapJunctions HeS3 cyt pA+ J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469,LID8470 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPamJunctions HeS3 cyt pA- J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPamJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapJunctions HeS3 cel pA+ J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633,LID16634 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPamJunctions HeS3 cel pA- J HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790,LID8791 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPamJunctions Junctions cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions HeLa-S3 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapJunctions CD20 cel pA+ J CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44498,LID44499 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapJunctions Junctions B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions CD20+ whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamJunctions CD20 cel pA- J CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44659,LID44660 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamJunctions Junctions B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions CD20+ whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapJunctions A549 nuc pA+ J A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45899,LID45900 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapJunctions Junctions epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions A549 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapJunctions A549 cyt pA+ J A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45897,LID45898 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapJunctions Junctions epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions A549 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapJunctions A549 cel pA+ J A549 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963,LID8964 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapJunctions Junctions epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions A549 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPamJunctions A549 cel pA- J A549 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005,LID9006 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPamJunctions Junctions epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions A549 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapJunctions K562 nuc pA+ J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556,LID8557 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPamJunctions K562 nuc pA- J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195,LID9196 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPamJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalJunctions K562 ncpm tot J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189,LID9190 iIDR nucleoplasm 2x76D total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 nucleoplasm total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapJunctions K562 cyt pA+ J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8465,LID8466 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPamJunctions K562 cyt pA- J K562 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545,LID18546 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPamJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalJunctions K562 chrm tot J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185,LID9186 iIDR chromatin 2x76D total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 chromatin total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapJunctions K562 cel pA+ J K562 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627,LID16628 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPamJunctions K562 cel pA- J K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659,LID8660 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPamJunctions Junctions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions K562 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapJunctions H1hSC nuc pA+ J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPamJunctions H1hSC nuc pA- J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPamJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapJunctions H1hSC cyt pA+ J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPamJunctions H1hSC cyt pA- J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPamJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapJunctions H1hSC cel pA+ J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461,LID8462 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPamJunctions H1hSC cel pA- J H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663,LID8664 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPamJunctions Junctions embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions H1-hESC whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapJunctions GM78 nuc pA+ J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532,LID8533 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 nucleus polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPamJunctions GM78 nuc pA- J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197,LID9198 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPamJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 nucleus polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalJunctions GM78 nlus tot J GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47963,LID47964 iIDR nucleolus 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 nucleolus total RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapJunctions GM78 cyt pA+ J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467,LID8468 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 cytosol polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPamJunctions GM78 cyt pA- J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547,LID18548 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPamJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 cytosol polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapJunctions GM78 cel pA+ J GM12878 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629,LID16630 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 whole cell polyA+ RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPamJunctions GM78 cel pA- J GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661,LID8662 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPamJunctions Junctions B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions GM12878 whole cell polyA- RNA-seq Junctions Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqViewPlusSig Plus Signal Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapPlusRawSigRep2 SKRA cel pA+ + 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8968 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapPlusRawSigRep2 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH RA whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapPlusRawSigRep1 SKRA cel pA+ + 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapPlusRawSigRep1 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH RA whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep2 SKRA cel pA- + 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9011 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep2 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH RA whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep1 SKRA cel pA- + 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaPlusRawSigRep1 PlusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand SK-N-SH RA whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc812190217CellTotalPlusRep2 SkMC cel tot + 2 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47246 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc812190217CellTotalPlusRep2 PlusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SkMC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc9011302CellTotalPlusRep1 SkMC cel tot + 1 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47245 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc9011302CellTotalPlusRep1 PlusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SkMC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapPlusRawSigRep2 NHLF cel pA+ + 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8701 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapPlusRawSigRep2 PlusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHLF whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapPlusRawSigRep1 NHLF cel pA+ + 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapPlusRawSigRep1 PlusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHLF whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaPlusRawSigRep2 NHLF cel pA- + 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8829 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaPlusRawSigRep2 PlusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHLF whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaPlusRawSigRep1 NHLF cel pA- + 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaPlusRawSigRep1 PlusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHLF whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm270110012CellTotalPlusRep2 NHMM2 cel tot + 2 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47259 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm270110012CellTotalPlusRep2 PlusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM M2 whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm27012303CellTotalPlusRep1 NHMM2 cel tot + 1 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47258 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm27012303CellTotalPlusRep1 PlusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM M2 whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalPlusRep2 NHMf cel tot + 2 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47257 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalPlusRep2 PlusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM.f M2 whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalPlusRep1 NHMf cel tot + 1 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47256 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalPlusRep1 PlusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHEM.f M2 whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapPlusRawSigRep4 NHEK nuc pA+ + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8798 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapPlusRawSigRep4 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapPlusRawSigRep3 NHEK nuc pA+ + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapPlusRawSigRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep4 NHEK nuc pA- + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9205 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep4 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep3 NHEK nuc pA- + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaPlusRawSigRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep4 NHEK cyt pA+ + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8796 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep4 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep3 NHEK cyt pA+ + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapPlusRawSigRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaPlusRawSigRep3 NHEK cyt pA- + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaPlusRawSigRep3 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep2 NHEK cel pA+ + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16632 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep2 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep1 NHEK cel pA+ + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16631 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapPlusRawSigRep1 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep2 NHEK cel pA- + 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8666 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep2 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep1 NHEK cel pA- + 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8665 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaPlusRawSigRep1 PlusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand NHEK whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf00608013CellTotalPlusRep2 NHDF cel tot + 2 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47248 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf00608013CellTotalPlusRep2 PlusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHDF whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf70717012CellTotalPlusRep1 NHDF cel tot + 1 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47247 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf70717012CellTotalPlusRep1 PlusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand NHDF whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp0092205CellTotalPlusRep2 HWP cel tot + 2 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47255 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp0092205CellTotalPlusRep2 PlusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HWP whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp81202015CellTotalPlusRep1 HWP cel tot + 1 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47254 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp81202015CellTotalPlusRep1 PlusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HWP whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf61004013CellTotalPlusRep2 HVMF cel tot + 2 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47250 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf61004013CellTotalPlusRep2 PlusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HVMF whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf60912033CellTotalPlusRep1 HVMF cel tot + 1 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47249 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf60912033CellTotalPlusRep1 PlusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HVMF whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep2 HSMM cel pA+ + 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8711 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep2 PlusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HSMM whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep1 HSMM cel pA+ + 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapPlusRawSigRep1 PlusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HSMM whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep2 HSMM cel pA- + 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8827 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep2 PlusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HSMM whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep1 HSMM cel pA- + 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaPlusRawSigRep1 PlusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HSMM whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalPlusRep2 HSVEC cel tot + 2 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47261 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalPlusRep2 PlusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HSaVEC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalPlusRep1 HSVEC cel tot + 1 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47260 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalPlusRep1 PlusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HSaVEC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalPlusRep2 HPIEC cel tot + 2 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47253 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalPlusRep2 PlusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPIEpC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalPlusRep1 HPIEC cel tot + 1 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47105 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalPlusRep1 PlusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPIEpC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalPlusRep2 HPCPL cel tot + 2 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47104 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalPlusRep2 PlusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPC-PL whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalPlusRep1 HPCPL cel tot + 1 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47301 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalPlusRep1 PlusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HPC-PL whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob00902021CellTotalPlusRep2 HOB cel tot + 2 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47252 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob00902021CellTotalPlusRep2 PlusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HOB whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob0091301CellTotalPlusRep1 HOB cel tot + 1 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47251 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob0091301CellTotalPlusRep1 PlusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HOB whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalPlusRep2 hMSUC cel tot + 2 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47300 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalPlusRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-UC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalPlusRep1 hMSUC cel tot + 1 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47299 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalPlusRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-UC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalPlusRep2 hMSBM cel tot + 2 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47100 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalPlusRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-BM whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalPlusRep1 hMSBM cel tot + 1 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47099 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalPlusRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-BM whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat906160112CellTotalPlusRep2 hMSAT cel tot + 2 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47098 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat906160112CellTotalPlusRep2 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-AT whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat010260412CellTotalPlusRep1 hMSAT cel tot + 1 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47097 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat010260412CellTotalPlusRep1 PlusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMSC-AT whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalPlusSignalRep1V2 hMNPB cel tot + 1 hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002878 2878 GSM984606 Gingeras CSHL LID47807 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalPlusSignalRep1V2 PlusSignal Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand hMNC-PB whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalPlusRep1 HMEpC cel tot + 1 HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002683 2683 GSM984621 Gingeras CSHL LID47096 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalPlusRep1 PlusSignal Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HMEpC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapPlusRawSigRep1 HMEC cel pA+ + 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapPlusRawSigRep1 PlusSignal mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HMEC whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaPlusRawSigRep1 HMEC cel pA- + 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaPlusRawSigRep1 PlusSignal mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HMEC whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalPlusRep2 HFDPC cel tot + 2 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47095 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalPlusRep2 PlusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HFDPC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalPlusRep1 HFDPC cel tot + 1 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47094 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalPlusRep1 PlusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HFDPC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch81008082CellTotalPlusRep2 HCH cel tot + 2 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47025 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch81008082CellTotalPlusRep2 PlusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HCH whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch00113082pCellTotalPlusRep1 HCH cel tot + 1 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47024 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch00113082pCellTotalPlusRep1 PlusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HCH whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalPlusRep2 HAoEC cel tot + 2 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47023 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalPlusRep2 PlusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoEC whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoec70717061CellTotalPlusRep1 HAoEC cel tot + 1 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47022 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoec70717061CellTotalPlusRep1 PlusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoEC whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalPlusRep2 HAoAF cel tot + 2 HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47021 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalPlusRep2 PlusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoAF whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalPlusSignalRep1 HAoAF cel tot + 1 HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47020 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalPlusSignalRep1 PlusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand HAoAF whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalPlusRep1 CD34 cel tot + 1 CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002670 2670 GSM981257 Gingeras CSHL LID45901 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalPlusRep1 PlusSignal hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand CD34+ Mobilized whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep2 BJ cel pA+ + 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8970 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep2 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep1 BJ cel pA+ + 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep1 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep2 BJ cel pA- + 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9008 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep2 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep1 BJ cel pA- + 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep1 PlusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand BJ whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep2 AG50 cel pA+ + 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8966 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep2 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep1 AG50 cel pA+ + 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep1 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep2 AG50 cel pA- + 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9002 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep2 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep1 AG50 cel pA- + 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep1 PlusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand AG04450 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapPlusRep4 SKNSH nuc pA+ + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46597 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapPlusRep3 SKNSH nuc pA+ + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46596 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapPlusRep4 SKNSH cyt pA+ + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46595 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapPlusRep3 SKNSH cyt pA+ + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46594 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapPlusRep4 SKNSH cel pA+ + 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46599 cell 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapPlusRep4 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapPlusRep3 SKNSH cel pA+ + 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46598 cell 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapPlusRep3 PlusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand SK-N-SH whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapPlusRep2 CD14 cel pA+ + 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44497 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapPlusRep2 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MonocytesCD14+ whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapPlusRep1 CD14 cel pA+ + 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44594 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapPlusRep1 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MonocytesCD14+ whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamPlusRep2 CD14 cel pA- + 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44658 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamPlusRep2 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MonocytesCD14+ whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamPlusRep1 CD14 cel pA- + 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44657 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamPlusRep1 PlusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MonocytesCD14+ whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep4 MCF7 nuc pA+ + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46860 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep3 MCF7 nuc pA+ + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46859 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep4 MCF7 cyt pA+ + 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46858 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep4 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep3 MCF7 cyt pA+ + 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46857 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep3 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand MCF-7 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep2 MCF7 cel pA+ + 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8687 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep2 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep1 MCF7 cel pA+ + 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep1 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep2 MCF7 cel pA- + 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8825 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep2 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep1 MCF7 cel pA- + 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep1 PlusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand MCF-7 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapPlusRep2 IMR90 nuc pA+ + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45635 nucleus 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapPlusRep1 IMR90 nuc pA+ + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45613 nucleus 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapPlusRep2 IMR90 cyt pA+ + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45612 cytosol 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapPlusRep1 IMR90 cyt pA+ + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45611 cytosol 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalPlusRep2 IMR90 cel tot + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45239 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalPlusRep1 IMR90 cel tot + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45238 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapPlusRep2 IMR90 cel pA+ + 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45017 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapPlusRep2 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapPlusRep1 IMR90 cel pA+ + 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45016 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapPlusRep1 PlusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand IMR90 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapPlusRawSigRep4 HUVEC nuc pA+ + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8691 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapPlusRawSigRep4 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapPlusRawSigRep3 HUVEC nuc pA+ + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapPlusRawSigRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaPlusRawSigRep4 HUVEC nuc pA- + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9207 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaPlusRawSigRep4 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaPlusRawSigRep3 HUVEC nuc pA- + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaPlusRawSigRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapPlusRawSigRep4 HUVEC cyt pA+ + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8689 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapPlusRawSigRep4 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapPlusRawSigRep3 HUVEC cyt pA+ + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapPlusRawSigRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaPlusRawSigRep3 HUVEC cyt pA- + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaPlusRawSigRep3 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapPlusRawSigRep2 HUVEC cel pA+ + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8464 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapPlusRawSigRep2 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapPlusRawSigRep1 HUVEC cel pA+ + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapPlusRawSigRep1 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaPlusRawSigRep2 HUVEC cel pA- + 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8789 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaPlusRawSigRep2 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaPlusRawSigRep1 HUVEC cel pA- + 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaPlusRawSigRep1 PlusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HUVEC whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapPlusRawSigRep2 HeG2 nuc pA+ + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8535 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapPlusRawSigRep1 HeG2 nuc pA+ + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep2 HeG2 nuc pA- + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9203 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep1 HeG2 nuc pA- + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep2 HeG2 cyt pA+ + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8472 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep1 HeG2 cyt pA+ + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep2 HeG2 cyt pA- + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18553 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep1 HeG2 cyt pA- + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep2 HeG2 cel pA+ + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16636 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep1 HeG2 cel pA+ + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaPlusRawSigRep2 HeG2 cel pA- + 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8793 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaPlusRawSigRep2 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaPlusRawSigRep1 HeG2 cel pA- + 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaPlusRawSigRep1 PlusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HepG2 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep2 HeS3 nuc pA+ + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8560 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep1 HeS3 nuc pA+ + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep2 HeS3 nuc pA- + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9201 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep1 HeS3 nuc pA- + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapPlusRawSigRep2 HeS3 cyt pA+ + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8470 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapPlusRawSigRep1 HeS3 cyt pA+ + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaPlusRawSigRep2 HeS3 cyt pA- + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep2 HeS3 cel pA+ + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16634 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep1 HeS3 cel pA+ + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaPlusRawSigRep2 HeS3 cel pA- + 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8791 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaPlusRawSigRep2 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaPlusRawSigRep1 HeS3 cel pA- + 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaPlusRawSigRep1 PlusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand HeLa-S3 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapPlusRep2 CD20 cel pA+ + 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44499 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapPlusRep2 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapPlusRep1 CD20 cel pA+ + 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44498 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapPlusRep1 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamPlusRep2 CD20 cel pA- + 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamPlusRep2 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamPlusRep1 CD20 cel pA- + 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamPlusRep1 PlusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand CD20+ whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapPlusRep4 A549 nuc pA+ + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45900 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapPlusRep3 A549 nuc pA+ + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45899 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapPlusRep4 A549 cyt pA+ + 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45898 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapPlusRep4 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapPlusRep3 A549 cyt pA+ + 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45897 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapPlusRep3 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand A549 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep2 A549 cel pA+ + 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8964 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep2 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep1 A549 cel pA+ + 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep1 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep2 A549 cel pA- + 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9006 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep2 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep1 A549 cel pA- + 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep1 PlusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand A549 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapPlusRawSigRep2 K562 nuc pA+ + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8557 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapPlusRawSigRep1 K562 nuc pA+ + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaPlusRawSigRep2 K562 nuc pA- + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9196 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaPlusRawSigRep1 K562 nuc pA- + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep4 K562 ncpm tot + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9190 nucleoplasm 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep4 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleoplasm total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep3 K562 ncpm tot + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189 nucleoplasm 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalPlusRawSigRep3 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleoplasm total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleolusTotalPlusRawSigRep4 K562 nlus tot + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000181 181 GSM765393 Gingeras CSHL LID9188 nucleolus 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleolusTotalPlusRawSigRep4 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 nucleolus total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapPlusRawSigRep2 K562 cyt pA+ + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8466 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapPlusRawSigRep1 K562 cyt pA+ + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2009-07-06 2010-04-06 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8465 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaPlusRawSigRep2 K562 cyt pA- + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18546 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaPlusRawSigRep1 K562 cyt pA- + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalPlusRawSigRep4 K562 chrm tot + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9186 chromatin 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalPlusRawSigRep4 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 chromatin total RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalPlusRawSigRep3 K562 chrm tot + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185 chromatin 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalPlusRawSigRep3 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 chromatin total RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapPlusRawSigRep2 K562 cel pA+ + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16628 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapPlusRawSigRep1 K562 cel pA+ + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaPlusRawSigRep2 K562 cel pA- + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaPlusRawSigRep2 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaPlusRawSigRep1 K562 cel pA- + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaPlusRawSigRep1 PlusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand K562 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapPlusRawSigRep2 H1hSC nuc pA+ + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaPlusRawSigRep2 H1hSC nuc pA- + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapPlusRawSigRep2 H1hSC cyt pA+ + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaPlusRawSigRep2 H1hSC cyt pA- + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapPlusRawSigRep2 H1hSC cel pA+ + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8462 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapPlusRawSigRep1 H1hSC cel pA+ + 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapPlusRawSigRep1 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaPlusRawSigRep2 H1hSC cel pA- + 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8664 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaPlusRawSigRep2 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaPlusRawSigRep1 H1hSC cel pA- + 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaPlusRawSigRep1 PlusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapPlusRawSigRep2 GM78 nuc pA+ + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8533 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapPlusRawSigRep1 GM78 nuc pA+ + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep2 GM78 nuc pA- + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9198 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep1 GM78 nuc pA- + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 nucleus polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalPlusSignalRep4 GM78 nlus tot + 4 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-28 2013-03-28 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47964 nucleolus 2x101D 4 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalPlusSignalRep4 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand GM12878 nucleolus total RNA-seq Plus signal Rep 4 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalPlusSignalRep3 GM78 nlus tot + 3 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47963 nucleolus 2x101D 3 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalPlusSignalRep3 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the plus strand GM12878 nucleolus total RNA-seq Plus signal Rep 3 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep2 GM78 cyt pA+ + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8468 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep1 GM78 cyt pA+ + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaPlusRawSigRep2 GM78 cyt pA- + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18548 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaPlusRawSigRep1 GM78 cyt pA- + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep2 GM78 cel pA+ + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16630 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA+ RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep1 GM78 cel pA+ + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA+ RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep2 GM78 cel pA- + 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8662 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep2 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA- RNA-seq Plus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep1 GM78 cel pA- + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep1 PlusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the plus strand GM12878 whole cell polyA- RNA-seq Plus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqViewMinusSig Minus Signal Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapMinusRawSigRep2 SKRA cel pA+ - 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8968 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapMinusRawSigRep2 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH RA whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapMinusRawSigRep1 SKRA cel pA+ - 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapMinusRawSigRep1 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH RA whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep2 SKRA cel pA- - 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9011 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep2 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH RA whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep1 SKRA cel pA- - 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaMinusRawSigRep1 MinusSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand SK-N-SH RA whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc812190217CellTotalMinusRep2 SkMC cel tot - 2 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47246 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc812190217CellTotalMinusRep2 MinusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SkMC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc9011302CellTotalMinusRep1 SkMC cel tot - 1 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47245 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc9011302CellTotalMinusRep1 MinusSignal Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SkMC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapMinusRawSigRep2 NHLF cel pA+ - 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8701 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapMinusRawSigRep2 MinusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHLF whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapMinusRawSigRep1 NHLF cel pA+ - 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapMinusRawSigRep1 MinusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHLF whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaMinusRawSigRep2 NHLF cel pA- - 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8829 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaMinusRawSigRep2 MinusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHLF whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaMinusRawSigRep1 NHLF cel pA- - 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaMinusRawSigRep1 MinusSignal lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHLF whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm270110012CellTotalMinusRep2 NHMM2 cel tot - 2 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47259 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm270110012CellTotalMinusRep2 MinusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM M2 whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm27012303CellTotalMinusRep1 NHMM2 cel tot - 1 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47258 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm27012303CellTotalMinusRep1 MinusSignal Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM M2 whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalMinusRep2 NHMf cel tot - 2 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47257 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalMinusRep2 MinusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM.f M2 whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalMinusRep1 NHMf cel tot - 1 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47256 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalMinusRep1 MinusSignal Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHEM.f M2 whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapMinusRawSigRep4 NHEK nuc pA+ - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8798 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapMinusRawSigRep4 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapMinusRawSigRep3 NHEK nuc pA+ - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapMinusRawSigRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep4 NHEK nuc pA- - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9205 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep4 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep3 NHEK nuc pA- - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaMinusRawSigRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep4 NHEK cyt pA+ - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8796 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep4 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep3 NHEK cyt pA+ - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapMinusRawSigRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaMinusRawSigRep3 NHEK cyt pA- - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaMinusRawSigRep3 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep2 NHEK cel pA+ - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16632 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep2 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep1 NHEK cel pA+ - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16631 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapMinusRawSigRep1 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep2 NHEK cel pA- - 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8666 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep2 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep1 NHEK cel pA- - 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8665 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaMinusRawSigRep1 MinusSignal epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand NHEK whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf00608013CellTotalMinusRep2 NHDF cel tot - 2 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47248 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf00608013CellTotalMinusRep2 MinusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHDF whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf70717012CellTotalMinusRep1 NHDF cel tot - 1 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47247 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf70717012CellTotalMinusRep1 MinusSignal Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand NHDF whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp0092205CellTotalMinusRep2 HWP cel tot - 2 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47255 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp0092205CellTotalMinusRep2 MinusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HWP whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp81202015CellTotalMinusRep1 HWP cel tot - 1 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47254 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp81202015CellTotalMinusRep1 MinusSignal Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HWP whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf61004013CellTotalMinusRep2 HVMF cel tot - 2 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47250 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf61004013CellTotalMinusRep2 MinusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HVMF whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf60912033CellTotalMinusRep1 HVMF cel tot - 1 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47249 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf60912033CellTotalMinusRep1 MinusSignal villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HVMF whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep2 HSMM cel pA+ - 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8711 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep2 MinusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HSMM whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep1 HSMM cel pA+ - 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapMinusRawSigRep1 MinusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HSMM whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep2 HSMM cel pA- - 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8827 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep2 MinusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HSMM whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep1 HSMM cel pA- - 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaMinusRawSigRep1 MinusSignal skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HSMM whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalMinusRep2 HSVEC cel tot - 2 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47261 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalMinusRep2 MinusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HSaVEC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalMinusRep1 HSVEC cel tot - 1 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47260 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalMinusRep1 MinusSignal Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HSaVEC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalMinusRep2 HPIEC cel tot - 2 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47253 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalMinusRep2 MinusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPIEpC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalMinusRep1 HPIEC cel tot - 1 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47105 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalMinusRep1 MinusSignal Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPIEpC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalMinusRep2 HPCPL cel tot - 2 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47104 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalMinusRep2 MinusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPC-PL whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalMinusRep1 HPCPL cel tot - 1 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47301 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalMinusRep1 MinusSignal Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HPC-PL whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob00902021CellTotalMinusRep2 HOB cel tot - 2 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47252 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob00902021CellTotalMinusRep2 MinusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HOB whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob0091301CellTotalMinusRep1 HOB cel tot - 1 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47251 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob0091301CellTotalMinusRep1 MinusSignal Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HOB whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalMinusRep2 hMSUC cel tot - 2 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47300 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalMinusRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-UC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalMinusRep1 hMSUC cel tot - 1 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47299 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalMinusRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-UC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalMinusRep2 hMSBM cel tot - 2 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47100 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalMinusRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-BM whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalMinusRep1 hMSBM cel tot - 1 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47099 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalMinusRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-BM whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat906160112CellTotalMinusRep2 hMSAT cel tot - 2 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47098 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat906160112CellTotalMinusRep2 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-AT whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat010260412CellTotalMinusRep1 hMSAT cel tot - 1 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47097 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat010260412CellTotalMinusRep1 MinusSignal Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMSC-AT whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalMinusSignalRep1V2 hMNPB cel tot - 1 hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002878 2878 GSM984606 Gingeras CSHL LID47807 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalMinusSignalRep1V2 MinusSignal Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand hMNC-PB whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalMinusRep1 HMEpC cel tot - 1 HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002683 2683 GSM984621 Gingeras CSHL LID47096 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalMinusRep1 MinusSignal Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HMEpC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapMinusRawSigRep1 HMEC cel pA+ - 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapMinusRawSigRep1 MinusSignal mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HMEC whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaMinusRawSigRep1 HMEC cel pA- - 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaMinusRawSigRep1 MinusSignal mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HMEC whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalMinusRep2 HFDPC cel tot - 2 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47095 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalMinusRep2 MinusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HFDPC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalMinusRep1 HFDPC cel tot - 1 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47094 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalMinusRep1 MinusSignal Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HFDPC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch81008082CellTotalMinusRep2 HCH cel tot - 2 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47025 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch81008082CellTotalMinusRep2 MinusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HCH whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch00113082pCellTotalMinusRep1 HCH cel tot - 1 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47024 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch00113082pCellTotalMinusRep1 MinusSignal Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HCH whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalMinusRep2 HAoEC cel tot - 2 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47023 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalMinusRep2 MinusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoEC whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoec70717061CellTotalMinusRep1 HAoEC cel tot - 1 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47022 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoec70717061CellTotalMinusRep1 MinusSignal Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoEC whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalMinusRep2 HAoAF cel tot - 2 HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47021 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalMinusRep2 MinusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoAF whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalMinusSignalRep1 HAoAF cel tot - 1 HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47020 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalMinusSignalRep1 MinusSignal Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand HAoAF whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalMinusRep1 CD34 cel tot - 1 CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002670 2670 GSM981257 Gingeras CSHL LID45901 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalMinusRep1 MinusSignal hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand CD34+ Mobilized whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep2 BJ cel pA+ - 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8970 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep2 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep1 BJ cel pA+ - 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep1 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep2 BJ cel pA- - 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9008 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep2 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep1 BJ cel pA- - 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep1 MinusSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand BJ whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep2 AG50 cel pA+ - 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8966 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep2 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep1 AG50 cel pA+ - 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep1 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep2 AG50 cel pA- - 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9002 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep2 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep1 AG50 cel pA- - 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep1 MinusSignal fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand AG04450 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapMinusRep4 SKNSH nuc pA+ - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46597 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapMinusRep3 SKNSH nuc pA+ - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46596 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapMinusRep4 SKNSH cyt pA+ - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46595 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapMinusRep3 SKNSH cyt pA+ - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46594 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapMinusRep4 SKNSH cel pA+ - 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46599 cell 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapMinusRep4 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapMinusRep3 SKNSH cel pA+ - 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46598 cell 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapMinusRep3 MinusSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand SK-N-SH whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapMinusRep2 CD14 cel pA+ - 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44497 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapMinusRep2 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MonocytesCD14+ whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapMinusRep1 CD14 cel pA+ - 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44594 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapMinusRep1 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MonocytesCD14+ whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamMinusRep2 CD14 cel pA- - 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44658 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamMinusRep2 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MonocytesCD14+ whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamMinusRep1 CD14 cel pA- - 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44657 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamMinusRep1 MinusSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MonocytesCD14+ whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep4 MCF7 nuc pA+ - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46860 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep3 MCF7 nuc pA+ - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46859 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep4 MCF7 cyt pA+ - 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46858 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep4 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep3 MCF7 cyt pA+ - 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46857 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep3 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand MCF-7 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep2 MCF7 cel pA+ - 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8687 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep2 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep1 MCF7 cel pA+ - 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep1 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep2 MCF7 cel pA- - 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8825 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep2 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep1 MCF7 cel pA- - 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep1 MinusSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand MCF-7 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapMinusRep2 IMR90 nuc pA+ - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45635 nucleus 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapMinusRep1 IMR90 nuc pA+ - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45613 nucleus 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapMinusRep2 IMR90 cyt pA+ - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45612 cytosol 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapMinusRep1 IMR90 cyt pA+ - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45611 cytosol 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalMinusRep2 IMR90 cel tot - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45239 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalMinusRep1 IMR90 cel tot - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45238 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapMinusRep2 IMR90 cel pA+ - 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45017 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapMinusRep2 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapMinusRep1 IMR90 cel pA+ - 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45016 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapMinusRep1 MinusSignal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand IMR90 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapMinusRawSigRep4 HUVEC nuc pA+ - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8691 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapMinusRawSigRep4 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapMinusRawSigRep3 HUVEC nuc pA+ - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapMinusRawSigRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaMinusRawSigRep4 HUVEC nuc pA- - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9207 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaMinusRawSigRep4 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaMinusRawSigRep3 HUVEC nuc pA- - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaMinusRawSigRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapMinusRawSigRep4 HUVEC cyt pA+ - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8689 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapMinusRawSigRep4 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapMinusRawSigRep3 HUVEC cyt pA+ - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapMinusRawSigRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaMinusRawSigRep3 HUVEC cyt pA- - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaMinusRawSigRep3 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapMinusRawSigRep2 HUVEC cel pA+ - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8464 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapMinusRawSigRep2 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapMinusRawSigRep1 HUVEC cel pA+ - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapMinusRawSigRep1 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaMinusRawSigRep2 HUVEC cel pA- - 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8789 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaMinusRawSigRep2 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaMinusRawSigRep1 HUVEC cel pA- - 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaMinusRawSigRep1 MinusSignal umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HUVEC whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapMinusRawSigRep2 HeG2 nuc pA+ - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8535 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapMinusRawSigRep1 HeG2 nuc pA+ - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep2 HeG2 nuc pA- - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9203 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep1 HeG2 nuc pA- - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep2 HeG2 cyt pA+ - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8472 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep1 HeG2 cyt pA+ - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep2 HeG2 cyt pA- - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18553 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep1 HeG2 cyt pA- - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep2 HeG2 cel pA+ - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16636 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep1 HeG2 cel pA+ - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaMinusRawSigRep2 HeG2 cel pA- - 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8793 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaMinusRawSigRep2 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaMinusRawSigRep1 HeG2 cel pA- - 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaMinusRawSigRep1 MinusSignal hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HepG2 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep2 HeS3 nuc pA+ - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8560 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep1 HeS3 nuc pA+ - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep2 HeS3 nuc pA- - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9201 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep1 HeS3 nuc pA- - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapMinusRawSigRep2 HeS3 cyt pA+ - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8470 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapMinusRawSigRep1 HeS3 cyt pA+ - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaMinusRawSigRep2 HeS3 cyt pA- - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep2 HeS3 cel pA+ - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16634 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep1 HeS3 cel pA+ - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaMinusRawSigRep2 HeS3 cel pA- - 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8791 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaMinusRawSigRep2 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaMinusRawSigRep1 HeS3 cel pA- - 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaMinusRawSigRep1 MinusSignal cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand HeLa-S3 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapMinusRep2 CD20 cel pA+ - 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44499 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapMinusRep2 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapMinusRep1 CD20 cel pA+ - 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44498 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapMinusRep1 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamMinusRep2 CD20 cel pA- - 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamMinusRep2 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamMinusRep1 CD20 cel pA- - 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamMinusRep1 MinusSignal B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand CD20+ whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapMinusRep4 A549 nuc pA+ - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45900 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapMinusRep3 A549 nuc pA+ - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45899 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapMinusRep4 A549 cyt pA+ - 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45898 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapMinusRep4 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapMinusRep3 A549 cyt pA+ - 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45897 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapMinusRep3 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand A549 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep2 A549 cel pA+ - 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8964 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep2 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep1 A549 cel pA+ - 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep1 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep2 A549 cel pA- - 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9006 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep2 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep1 A549 cel pA- - 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep1 MinusSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand A549 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapMinusRawSigRep2 K562 nuc pA+ - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8557 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapMinusRawSigRep1 K562 nuc pA+ - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaMinusRawSigRep2 K562 nuc pA- - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9196 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaMinusRawSigRep1 K562 nuc pA- - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep4 K562 ncpm tot - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9190 nucleoplasm 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep4 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleoplasm total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep3 K562 ncpm tot - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189 nucleoplasm 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalMinusRawSigRep3 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleoplasm total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleolusTotalMinusRawSigRep4 K562 nlus tot - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000181 181 GSM765393 Gingeras CSHL LID9188 nucleolus 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleolusTotalMinusRawSigRep4 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 nucleolus total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapMinusRawSigRep2 K562 cyt pA+ - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8466 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapMinusRawSigRep1 K562 cyt pA+ - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2009-07-06 2010-04-06 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8465 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaMinusRawSigRep2 K562 cyt pA- - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18546 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaMinusRawSigRep1 K562 cyt pA- - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalMinusRawSigRep4 K562 chrm tot - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9186 chromatin 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalMinusRawSigRep4 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 chromatin total RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalMinusRawSigRep3 K562 chrm tot - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185 chromatin 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalMinusRawSigRep3 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 chromatin total RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapMinusRawSigRep2 K562 cel pA+ - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16628 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapMinusRawSigRep1 K562 cel pA+ - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaMinusRawSigRep2 K562 cel pA- - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaMinusRawSigRep2 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaMinusRawSigRep1 K562 cel pA- - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaMinusRawSigRep1 MinusSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand K562 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapMinusRawSigRep2 H1hSC nuc pA+ - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaMinusRawSigRep2 H1hSC nuc pA- - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapMinusRawSigRep2 H1hSC cyt pA+ - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaMinusRawSigRep2 H1hSC cyt pA- - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapMinusRawSigRep2 H1hSC cel pA+ - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8462 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapMinusRawSigRep1 H1hSC cel pA+ - 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapMinusRawSigRep1 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaMinusRawSigRep2 H1hSC cel pA- - 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8664 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaMinusRawSigRep2 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaMinusRawSigRep1 H1hSC cel pA- - 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaMinusRawSigRep1 MinusSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapMinusRawSigRep2 GM78 nuc pA+ - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8533 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapMinusRawSigRep1 GM78 nuc pA+ - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep2 GM78 nuc pA- - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9198 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep1 GM78 nuc pA- - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 nucleus polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalMinusSignalRep4 GM78 nlus tot - 4 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-28 2013-03-28 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47964 nucleolus 2x101D 4 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalMinusSignalRep4 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand GM12878 nucleolus total RNA-seq Minus signal Rep 4 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalMinusSignalRep3 GM78 nlus tot - 3 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47963 nucleolus 2x101D 3 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalMinusSignalRep3 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Graphs the base-by-base density of tags on the minus strand GM12878 nucleolus total RNA-seq Minus signal Rep 3 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep2 GM78 cyt pA+ - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8468 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep1 GM78 cyt pA+ - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep2 GM78 cyt pA- - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18548 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep1 GM78 cyt pA- - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep2 GM78 cel pA+ - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16630 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA+ RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep1 GM78 cel pA+ - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA+ RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep2 GM78 cel pA- - 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8662 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep2 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA- RNA-seq Minus signal Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep1 GM78 cel pA- - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep1 MinusSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Graphs the base-by-base density of tags on the minus strand GM12878 whole cell polyA- RNA-seq Minus signal Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqViewContigs Contigs Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapContigs SKRA cel pA+ C SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967,LID8968 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapContigs Contigs neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH RA whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPamContigs SKRA cel pA- C SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003,LID9011 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPamContigs Contigs neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH RA whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmcCellTotalContigs SkMC cel tot C SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002678 2678 GSM984615 Gingeras CSHL LID47245,LID47246 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmcCellTotalContigs Contigs Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SkMC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapContigs NHLF cel pA+ C NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692,LID8701 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapContigs Contigs lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHLF whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPamContigs NHLF cel pA- C NHLF RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828,LID8829 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPamContigs Contigs lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHLF whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm2CellTotalContigs NHMM2 cel tot C NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002687 2687 GSM984617 Gingeras CSHL LID47258,LID47259 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm2CellTotalContigs Contigs Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEM M2 whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm2CellTotalContigs NHMf cel tot C NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002686 2686 GSM984616 Gingeras CSHL LID47256,LID47257 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm2CellTotalContigs Contigs Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEM.f M2 whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapContigs NHEK nuc pA+ C NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797,LID8798 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapContigs Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPamContigs NHEK nuc pA- C NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204,LID9205 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPamContigs Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapContigs NHEK cyt pA+ C NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795,LID8796 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapContigs Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPamContigsV2 NHEK cyt pA- C NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPamContigsV2 Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapContigsV2 NHEK cel pA+ C NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-05-14 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID8694 cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapContigsV2 Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPamContigsV2 NHEK cel pA- C NHEK RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8830 cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPamContigsV2 Contigs epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHEK whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdfCellTotalContigs NHDF cel tot C NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002677 2677 GSM984612 Gingeras CSHL LID47247,LID47248 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdfCellTotalContigs Contigs Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). NHDF whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwpCellTotalContigs HWP cel tot C HWP RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002682 2682 GSM984620 Gingeras CSHL LID47254,LID47255 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwpCellTotalContigs Contigs Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HWP whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmfCellTotalContigs HVMF cel tot C HVMF RnaSeq ENCODE Jul 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002681 2681 GSM984619 Gingeras CSHL LID47249,LID47250 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmfCellTotalContigs Contigs villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HVMF whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapContigs HSMM cel pA+ C HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710,LID8711 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapContigs Contigs skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HSMM whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPamContigs HSMM cel pA- C HSMM RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826,LID8827 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPamContigs Contigs skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HSMM whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalContigs HSVEC cel tot C HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002676 2676 GSM984613 Gingeras CSHL LID47261,LID47260 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalContigs Contigs Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HSaVEC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalContigs HPIEC cel tot C HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002685 2685 GSM984604 Gingeras CSHL LID47105,LID47253 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalContigs Contigs Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HPIEpC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalContigs HPCPL cel tot C HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002667 2667 GSM981255 Gingeras CSHL LID47301,LID47104 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalContigs Contigs Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HPC-PL whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHobCellTotalContigs HOB cel tot C HOB RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002675 2675 GSM984610 Gingeras CSHL LID47251,LID47252 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHobCellTotalContigs Contigs Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HOB whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscucCellTotalContigs hMSUC cel tot C hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002684 2684 GSM984607 Gingeras CSHL LID47299,LID47300 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscucCellTotalContigs Contigs Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMSC-UC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbmCellTotalContigs hMSBM cel tot C hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002673 2673 GSM984608 Gingeras CSHL LID47099,LID47100 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbmCellTotalContigs Contigs Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMSC-BM whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscatCellTotalContigs hMSAT cel tot C hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002669 2669 GSM981260 Gingeras CSHL LID47097,LID47098 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscatCellTotalContigs Contigs Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMSC-AT whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalContigsV2 hMNPB cel tot C hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-07-04 2013-04-04 wgEncodeEH002878 2878 GSM984606 Gingeras CSHL LID47807 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalContigsV2 Contigs Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). hMNC-PB whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalContigs HMEpC cel tot C HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002683 2683 GSM984621 Gingeras CSHL LID47096 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalContigs Contigs Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HMEpC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapContigsV2 HMEC cel pA+ C HMEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-05-14 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapContigsV2 Contigs mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HMEC whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPamContigsV2 HMEC cel pA- C HMEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPamContigsV2 Contigs mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HMEC whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpcCellTotalContigs HFDPC cel tot C HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002671 2671 GSM981258 Gingeras CSHL LID47094,LID47095 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpcCellTotalContigs Contigs Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HFDPC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHchCellTotalContigs HCH cel tot C HCH RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002674 2674 GSM984611 Gingeras CSHL LID47024,LID47025 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHchCellTotalContigs Contigs Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HCH whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalContigs HAoEC cel tot C HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002680 2680 GSM984618 Gingeras CSHL LID47022,LID47023 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalContigs Contigs Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HAoEC whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalContigs HAoAF cel tot C HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002679 2679 GSM984614 Gingeras CSHL LID47021,LID47020 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalContigs Contigs Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HAoAF whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalContigs CD34 cel tot C CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002670 2670 GSM981257 Gingeras CSHL LID45901 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalContigs Contigs hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). CD34+ Mobilized whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapContigs BJ cel pA+ C BJ RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969,LID8970 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapContigs Contigs skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). BJ whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPamContigs BJ cel pA- C BJ RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007,LID9008 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPamContigs Contigs skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). BJ whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapContigs AG50 cel pA+ C AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965,LID8966 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapContigs Contigs fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). AG04450 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPamContigs AG50 cel pA- C AG04450 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001,LID9002 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPamContigs Contigs fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). AG04450 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapContigs SKNSH nuc pA+ C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002631 2631 GSM981250 Gingeras CSHL LID46596,LID46597 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapContigs SKNSH cyt pA+ C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002630 2630 GSM981251 Gingeras CSHL LID46594,LID46595 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapContigs SKNSH cel pA+ C SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002632 2632 GSM981253 Gingeras CSHL LID46598,LID46599 iIDR cell 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapContigs Contigs neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). SK-N-SH whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapContigs CD14 cel pA+ C Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002672 2672 GSM984609 Gingeras CSHL LID44594,LID44497 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapContigs Contigs Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MonocytesCD14+ whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamContigs CD14 cel pA- C Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002668 2668 GSM981259 Gingeras CSHL LID44657,LID44658 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamContigs Contigs Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MonocytesCD14+ whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapContigs MCF7 nuc pA+ C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002627 2627 GSM981245 Gingeras CSHL LID46859,LID46860 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapContigs MCF7 cyt pA+ C MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002633 2633 GSM981252 Gingeras CSHL LID46857,LID46858 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapContigs MCF7 cel pA+ C MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686,LID8687 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPamContigs MCF7 cel pA- C MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824,LID8825 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPamContigs Contigs mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). MCF-7 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapContigs IMR90 nuc pA+ C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002628 2628 GSM981248 Gingeras CSHL LID45635,LID45613 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapContigs IMR90 cyt pA+ C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002626 2626 GSM981244 Gingeras CSHL LID45611,LID45612 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalContigs IMR90 cel tot C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002623 2623 GSM981243 Gingeras CSHL LID45238,LID45239 iIDR cell 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 whole cell total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapContigs IMR90 cel pA+ C IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002629 2629 GSM981249 Gingeras CSHL LID45016,LID45017 iIDR cell 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapContigs Contigs fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). IMR90 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapContigs HUVEC nuc pA+ C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690,LID8691 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPamContigs HUVEC nuc pA- C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206,LID9207 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPamContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapContigs HUVEC cyt pA+ C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688,LID8689 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPamContigsV2 HUVEC cyt pA- C HUVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPamContigsV2 Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapContigs HUVEC cel pA+ C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463,LID8464 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPamContigs HUVEC cel pA- C HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788,LID8789 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPamContigs Contigs umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HUVEC whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapContigs HeG2 nuc pA+ C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534,LID8535 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPamContigs HeG2 nuc pA- C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202,LID9203 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPamContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapContigs HeG2 cyt pA+ C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471,LID8472 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPamContigs HeG2 cyt pA- C HepG2 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552,LID18553 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPamContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapContigs HeG2 cel pA+ C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635,LID16636 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPamContigs HeG2 cel pA- C HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792,LID8793 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPamContigs Contigs hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HepG2 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapContigs HeS3 nuc pA+ C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559,LID8560 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPamContigs HeS3 nuc pA- C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200,LID9201 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPamContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapContigs HeS3 cyt pA+ C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469,LID8470 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPamContigsV2 HeS3 cyt pA- C HeLa-S3 RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPamContigsV2 Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapContigs HeS3 cel pA+ C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633,LID16634 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPamContigs HeS3 cel pA- C HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790,LID8791 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPamContigs Contigs cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). HeLa-S3 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapContigs CD20 cel pA+ C CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002665 2665 GSM981256 Gingeras CSHL LID44498,LID44499 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapContigs Contigs B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). CD20+ whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamContigs CD20 cel pA- C CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002666 2666 GSM981254 Gingeras CSHL LID44659,LID44660 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamContigs Contigs B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). CD20+ whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapContigs A549 nuc pA+ C A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002625 2625 GSM981247 Gingeras CSHL LID45899,LID45900 iIDR nucleus 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapContigs A549 cyt pA+ C A549 RnaSeq ENCODE Mar 2012 Freeze 2012-03-16 2012-05-14 wgEncodeEH002624 2624 GSM981246 Gingeras CSHL LID45897,LID45898 iIDR cytosol 2x101D longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapContigs A549 cel pA+ C A549 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963,LID8964 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPamContigs A549 cel pA- C A549 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005,LID9006 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPamContigs Contigs epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). A549 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapContigs K562 nuc pA+ C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556,LID8557 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPamContigs K562 nuc pA- C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195,LID9196 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPamContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalContigs K562 ncpm tot C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189,LID9190 iIDR nucleoplasm 2x76D total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 nucleoplasm total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapContigs K562 cyt pA+ C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000140 140 GSM840137 Gingeras CSHL LID8465,LID8466 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPamContigs K562 cyt pA- C K562 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545,LID18546 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPamContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalContigs K562 chrm tot C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185,LID9186 iIDR chromatin 2x76D total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 chromatin total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapContigs K562 cel pA+ C K562 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627,LID16628 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPamContigs K562 cel pA- C K562 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659,LID8660 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPamContigs Contigs leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). K562 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapContigsV2 H1hSC nuc pA+ C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-05-14 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPamContigsV2 H1hSC nuc pA- C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPamContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapContigsV2 H1hSC cyt pA+ C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-05-14 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPamContigsV2 H1hSC cyt pA- C H1-hESC RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-10 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPamContigsV2 Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapContigs H1hSC cel pA+ C H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461,LID8462 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapContigs Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPamContigs H1hSC cel pA- C H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663,LID8664 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPamContigs Contigs embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). H1-hESC whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapContigs GM78 nuc pA+ C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532,LID8533 iIDR nucleus 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 nucleus polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPamContigs GM78 nuc pA- C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197,LID9198 iIDR nucleus 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPamContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 nucleus polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalContigs GM78 nlus tot C GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEH003034 3034 GSM984605 Gingeras CSHL LID47963,LID47964 iIDR nucleolus 2x101D total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 nucleolus total RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapContigs GM78 cyt pA+ C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467,LID8468 iIDR cytosol 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 cytosol polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPamContigs GM78 cyt pA- C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547,LID18548 iIDR cytosol 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPamContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 cytosol polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapContigs GM78 cel pA+ C GM12878 RnaSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629,LID16630 iIDR cell 2x76D longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 whole cell polyA+ RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPamContigs GM78 cel pA- C GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-02-18 2011-11-18 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661,LID8662 iIDR cell 2x76D longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPamContigs Contigs B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). GM12878 whole cell polyA- RNA-seq Contigs Pooled from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqViewAlignments Alignments Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapAlnRep2 SKRA cel pA+ A 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8968 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapAlnRep2 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RA whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellPapAlnRep1 SKRA cel pA+ A 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000169 169 GSM765395 Gingeras CSHL LID8967 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellPapAlnRep1 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RA whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaAlnRep2 SKRA cel pA- A 2 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9011 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaAlnRep2 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RA whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaAlnRep1 SKRA cel pA- A 1 SK-N-SH_RA RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000197 197 GSM767845 Gingeras CSHL LID9003 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqSknshraCellLongnonpolyaAlnRep1 Alignments neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RA whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc812190217CellTotalAlnRep2 SkMC cel tot A 2 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002678 2678 Gingeras CSHL LID47246 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc812190217CellTotalAlnRep2 Alignments Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SkMC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSkmc9011302CellTotalAlnRep1 SkMC cel tot A 1 SkMC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002678 2678 Gingeras CSHL LID47245 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSkmc9011302CellTotalAlnRep1 Alignments Skeletal muscle myosatellite cells from two individuals, SkMC_9011302 SkMC_8121902.17 from M. pectoralis / Mm. intercostales Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SkMC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapAlnRep2 NHLF cel pA+ A 2 NHLF RnaSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8701 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapAlnRep2 Alignments lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellPapAlnRep1 NHLF cel pA+ A 1 NHLF RnaSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEH000168 168 GSM765394 Gingeras CSHL LID8692 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellPapAlnRep1 Alignments lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaAlnRep2 NHLF cel pA- A 2 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8829 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaAlnRep2 Alignments lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaAlnRep1 NHLF cel pA- A 1 NHLF RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000178 178 GSM765389 Gingeras CSHL LID8828 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhlfCellLongnonpolyaAlnRep1 Alignments lung fibroblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHLF whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm270110012CellTotalAlnRep2 NHMM2 cel tot A 2 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 Gingeras CSHL LID47259 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm270110012CellTotalAlnRep2 Alignments Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM M2 whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemm27012303CellTotalAlnRep1 NHMM2 cel tot A 1 NHEM_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002687 2687 Gingeras CSHL LID47258 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemm27012303CellTotalAlnRep1 Alignments Epidermal Melanocytes (adult) from two individuals, NHEM_M2_7011001.2 and NHEM_M2_7012303 from cheek / temple Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM M2 whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalAlnRep2 NHMf cel tot A 2 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 Gingeras CSHL LID47257 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm250713022CellTotalAlnRep2 Alignments Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM.f M2 whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalAlnRep1 NHMf cel tot A 1 NHEM.f_M2 RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002686 2686 Gingeras CSHL LID47256 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhemfm26022001CellTotalAlnRep1 Alignments Epidermal Melanocytes from two individuals, NHEM.f_M2_5071302.2 and NHEM.f_M2_6022001 from foreskin Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHEM.f M2 whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapAlnRep4 NHEK nuc pA+ A 2 NHEK RnaSeq ENCODE Mar 2012 Freeze 2011-06-08 2012-03-08 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8798 nucleus 2x76D 4 longPolyA Illumina_GA2x U wgEncodeCshlLongRnaSeqNhekNucleusPapAlnRep4 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusPapAlnRep3 NHEK nuc pA+ A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000165 165 GSM765399 Gingeras CSHL LID8797 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusPapAlnRep3 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaAlnRep4 NHEK nuc pA- A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9205 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaAlnRep4 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaAlnRep3 NHEK nuc pA- A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000196 196 GSM767846 Gingeras CSHL LID9204 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekNucleusLongnonpolyaAlnRep3 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapAlnRep4 NHEK cyt pA+ A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8796 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapAlnRep4 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolPapAlnRep3 NHEK cyt pA+ A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000166 166 GSM765400 Gingeras CSHL LID8795 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolPapAlnRep3 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaAlnRep3 NHEK cyt pA- A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000195 195 GSM767843 Gingeras CSHL LID18554 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCytosolLongnonpolyaAlnRep3 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK cytosol polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapAlnRep2 NHEK cel pA+ A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16632 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapAlnRep2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellPapAlnRep1 NHEK cel pA+ A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000167 167 GSM765401 Gingeras CSHL LID16631 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellPapAlnRep1 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaAlnRep2 NHEK cel pA- A 2 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8666 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaAlnRep2 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaAlnRep1 NHEK cel pA- A 1 NHEK RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000164 164 GSM765398 Gingeras CSHL LID8665 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqNhekCellLongnonpolyaAlnRep1 Alignments epidermal keratinocytes Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch NHEK whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf00608013CellTotalAlnRep2 NHDF cel tot A 2 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002677 2677 Gingeras CSHL LID47248 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf00608013CellTotalAlnRep2 Alignments Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHDF whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqNhdf70717012CellTotalAlnRep1 NHDF cel tot A 1 NHDF RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002677 2677 Gingeras CSHL LID47247 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqNhdf70717012CellTotalAlnRep1 Alignments Dermal Fibroblasts from temple / breast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch NHDF whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp0092205CellTotalAlnRep2 HWP cel tot A 2 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002682 2682 Gingeras CSHL LID47255 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp0092205CellTotalAlnRep2 Alignments Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HWP whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHwp81202015CellTotalAlnRep1 HWP cel tot A 1 HWP RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002682 2682 Gingeras CSHL LID47254 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHwp81202015CellTotalAlnRep1 Alignments Undifferentiated White Preadipocytes from two individuals, HWP_0092205 and HWP_8120201.5, subcutaneous adipose tissue from abdomen / upper arm Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HWP whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf61004013CellTotalAlnRep2 HVMF cel tot A 2 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002681 2681 Gingeras CSHL LID47250 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf61004013CellTotalAlnRep2 Alignments villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HVMF whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHvmf60912033CellTotalAlnRep1 HVMF cel tot A 1 HVMF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002681 2681 Gingeras CSHL LID47249 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHvmf60912033CellTotalAlnRep1 Alignments villous mesenchymal fibroblast cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HVMF whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapAlnRep2 HSMM cel pA+ A 2 HSMM RnaSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8711 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapAlnRep2 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellPapAlnRep1 HSMM cel pA+ A 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000154 154 GSM758578 Gingeras CSHL LID8710 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellPapAlnRep1 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaAlnRep2 HSMM cel pA- A 2 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8827 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaAlnRep2 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaAlnRep1 HSMM cel pA- A 1 HSMM RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000177 177 GSM765391 Gingeras CSHL LID8826 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHsmmCellLongnonpolyaAlnRep1 Alignments skeletal muscle myoblasts Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HSMM whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalAlnRep2 HSVEC cel tot A 2 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002676 2676 Gingeras CSHL LID47261 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalAlnRep2 Alignments Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HSaVEC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHsavecCellTotalAlnRep1 HSVEC cel tot A 1 HSaVEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002676 2676 Gingeras CSHL LID47260 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHsavecCellTotalAlnRep1 Alignments Saphenous Vein Endothelial Cells from two individuals, HSaVEC_9100101.15 and HSaVEC_0022202.16 from thigh Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HSaVEC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalAlnRep2 HPIEC cel tot A 2 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002685 2685 Gingeras CSHL LID47253 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalAlnRep2 Alignments Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPIEpC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpiepcCellTotalAlnRep1 HPIEC cel tot A 1 HPIEpC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002685 2685 Gingeras CSHL LID47105 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpiepcCellTotalAlnRep1 Alignments Placental Epithelial Cells amniotic membrane Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPIEpC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalAlnRep2 HPCPL cel tot A 2 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002667 2667 Gingeras CSHL LID47104 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalAlnRep2 Alignments Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPC-PL whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHpcplCellTotalAlnRep1 HPCPL cel tot A 1 HPC-PL RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002667 2667 Gingeras CSHL LID47301 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHpcplCellTotalAlnRep1 Alignments Undifferentiated Pericytes from HPC-PL_0032601.13 and HPC-PL_0101504.13 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HPC-PL whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob00902021CellTotalAlnRep2 HOB cel tot A 2 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002675 2675 Gingeras CSHL LID47252 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob00902021CellTotalAlnRep2 Alignments Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HOB whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHob0091301CellTotalAlnRep1 HOB cel tot A 1 HOB RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002675 2675 Gingeras CSHL LID47251 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHob0091301CellTotalAlnRep1 Alignments Undifferentiated Osteoblasts from two individuals, HOB_0090202.1 and HOB_0091301 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HOB whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalAlnRep2 hMSUC cel tot A 2 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002684 2684 Gingeras CSHL LID47300 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00811017CellTotalAlnRep2 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-UC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalAlnRep1 hMSUC cel tot A 1 hMSC-UC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002684 2684 Gingeras CSHL LID47299 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscuc00525017CellTotalAlnRep1 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-UC_0081101.7 and hMSC-UC_0052501.7 from matrix (Wharton's Jelly) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-UC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalAlnRep2 hMSBM cel tot A 2 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-25 wgEncodeEH002673 2673 Gingeras CSHL LID47100 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005060211CellTotalAlnRep2 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-BM whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalAlnRep1 hMSBM cel tot A 1 hMSC-BM RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002673 2673 Gingeras CSHL LID47099 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscbm005110511CellTotalAlnRep1 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-BM_0050602.11 and hMSC-BM_0051105.11 from femoral head Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-BM whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat906160112CellTotalAlnRep2 hMSAT cel tot A 2 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002669 2669 Gingeras CSHL LID47098 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat906160112CellTotalAlnRep2 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-AT whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmscat010260412CellTotalAlnRep1 hMSAT cel tot A 1 hMSC-AT RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002669 2669 Gingeras CSHL LID47097 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmscat010260412CellTotalAlnRep1 Alignments Undifferentiated Mesenchymal Stem Cells from two individuals, hMSC-AT_9061601.12 and hMSC-AT_0102604.12 from subcutaneous abdomen adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMSC-AT whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmncpbCellTotalAlnRep1V2 hMNPB cel tot A 1 hMNC-PB RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002878 2878 Gingeras CSHL LID47807 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmncpbCellTotalAlnRep1V2 Alignments Mononuclear Cells (peripheral blood-single donor) from two individuals, hMNC-PB_0022330.9 and hMNC-PB_0082430.9 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch hMNC-PB whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmepcCellTotalAlnRep1 HMEpC cel tot A 1 HMEpC RnaSeq ENCODE Mar 2012 Freeze 2012-02-26 2012-11-26 wgEncodeEH002683 2683 Gingeras CSHL LID47096 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHmepcCellTotalAlnRep1 Alignments Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HMEpC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellPapAlnRep1 HMEC cel pA+ A 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000153 153 GSM758571 Gingeras CSHL LID8695 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellPapAlnRep1 Alignments mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HMEC whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaAlnRep1 HMEC cel pA- A 1 HMEC RnaSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000176 176 GSM765397 Gingeras CSHL LID8831 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHmecCellLongnonpolyaAlnRep1 Alignments mammary epithelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HMEC whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalAlnRep2 HFDPC cel tot A 2 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002671 2671 Gingeras CSHL LID47095 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01005032CellTotalAlnRep2 Alignments Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HFDPC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalAlnRep1 HFDPC cel tot A 1 HFDPC RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002671 2671 Gingeras CSHL LID47094 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHfdpc01027033CellTotalAlnRep1 Alignments Follicle Dermal Papilla Cells from two individuals, HFDPC_0100503.2 and HFDPC_0102703.3 from lateral scalp (brown, blond) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HFDPC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch81008082CellTotalAlnRep2 HCH cel tot A 2 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 Gingeras CSHL LID47025 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch81008082CellTotalAlnRep2 Alignments Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HCH whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHch00113082pCellTotalAlnRep1 HCH cel tot A 1 HCH RnaSeq ENCODE Mar 2012 Freeze 2012-02-24 2012-11-24 wgEncodeEH002674 2674 Gingeras CSHL LID47024 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHch00113082pCellTotalAlnRep1 Alignments Undifferentiated Chondrocytes from two individuals, HCH_8100808.2 and HCH_0011308.2P from knee joint Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HCH whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoecCellTotalAlnRep2 HAoEC cel tot A 2 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-03-14 2012-12-14 wgEncodeEH002680 2680 Gingeras CSHL LID47023 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoecCellTotalAlnRep2 Alignments Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HAoEC whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoec70717061CellTotalAlnRep1 HAoEC cel tot A 1 HAoEC RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-25 wgEncodeEH002680 2680 Gingeras CSHL LID47022 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoec70717061CellTotalAlnRep1 Alignments Aortic Endothelial Cells (thoracic) from two individuals, HAoEC_7071706.1 and HAoEC_8061102.1 Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HAoEC whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalAlnRep2 HAoAF cel tot A 2 HAoAF RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-11-24 wgEncodeEH002679 2679 Gingeras CSHL LID47021 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoaf609010111CellTotalAlnRep2 Alignments Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HAoAF whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHaoafCellTotalAlnRep1 HAoAF cel tot A 1 HAoAF RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH002679 2679 Gingeras CSHL LID47020 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqHaoafCellTotalAlnRep1 Alignments Aortic Adventitial Fibroblasts from two individuals, HAoAF_6090101.11 and HAoAF_6111301.9 from tunica adventitia Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch HAoAF whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalAlnRep1 CD34 cel tot A 1 CD34+_Mobilized RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002670 2670 Gingeras CSHL LID45901 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqCd34mobilizedCellTotalAlnRep1 Alignments hematopoietic progenitor cells- mobilized, from donor RO01679. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch CD34+ Mobilized whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapAlnRep2 BJ cel pA+ A 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8970 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapAlnRep2 Alignments skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch BJ whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellPapAlnRep1 BJ cel pA+ A 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000145 145 GSM758562 Gingeras CSHL LID8969 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellPapAlnRep1 Alignments skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch BJ whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaAlnRep2 BJ cel pA- A 2 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9008 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaAlnRep2 Alignments skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch BJ whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqBjCellLongnonpolyaAlnRep1 BJ cel pA- A 1 BJ RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000185 185 GSM767855 Gingeras CSHL LID9007 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqBjCellLongnonpolyaAlnRep1 Alignments skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch BJ whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapAlnRep2 AG50 cel pA+ A 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8966 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapAlnRep2 Alignments fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch AG04450 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellPapAlnRep1 AG50 cel pA+ A 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000144 144 GSM758561 Gingeras CSHL LID8965 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellPapAlnRep1 Alignments fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch AG04450 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaAlnRep2 AG50 cel pA- A 2 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9002 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaAlnRep2 Alignments fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch AG04450 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaAlnRep1 AG50 cel pA- A 1 AG04450 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000179 179 GSM765396 Gingeras CSHL LID9001 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaAlnRep1 Alignments fetal lung fibroblast Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch AG04450 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapAlnRep4 SKNSH nuc pA+ A 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002631 2631 Gingeras CSHL LID46597 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapAlnRep4 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshNucleusPapAlnRep3 SKNSH nuc pA+ A 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002631 2631 Gingeras CSHL LID46596 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshNucleusPapAlnRep3 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapAlnRep4 SKNSH cyt pA+ A 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 Gingeras CSHL LID46595 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapAlnRep4 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCytosolPapAlnRep3 SKNSH cyt pA+ A 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002630 2630 Gingeras CSHL LID46594 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCytosolPapAlnRep3 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapAlnRep4 SKNSH cel pA+ A 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002632 2632 Gingeras CSHL LID46599 cell 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapAlnRep4 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqSknshCellPapAlnRep3 SKNSH cel pA+ A 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002632 2632 Gingeras CSHL LID46598 cell 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqSknshCellPapAlnRep3 Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapAlnRep2 CD14 cel pA+ A 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 Gingeras CSHL LID44497 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapAlnRep2 Alignments Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MonocytesCD14+ whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPapAlnRep1 CD14 cel pA+ A 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002672 2672 Gingeras CSHL LID44594 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPapAlnRep1 Alignments Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MonocytesCD14+ whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamAlnRep2 CD14 cel pA- A 2 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002668 2668 Gingeras CSHL LID44658 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamAlnRep2 Alignments Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MonocytesCD14+ whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMonocd14CellPamAlnRep1 CD14 cel pA- A 1 Monocytes-CD14+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002668 2668 Gingeras CSHL LID44657 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMonocd14CellPamAlnRep1 Alignments Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MonocytesCD14+ whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapAlnRep4 MCF7 nuc pA+ A 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002627 2627 Gingeras CSHL LID46860 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapAlnRep4 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7NucleusPapAlnRep3 MCF7 nuc pA+ A 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002627 2627 Gingeras CSHL LID46859 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7NucleusPapAlnRep3 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapAlnRep4 MCF7 cyt pA+ A 2 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-25 2012-05-14 wgEncodeEH002633 2633 Gingeras CSHL LID46858 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapAlnRep4 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CytosolPapAlnRep3 MCF7 cyt pA+ A 1 MCF-7 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002633 2633 Gingeras CSHL LID46857 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqMcf7CytosolPapAlnRep3 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapAlnRep2 MCF7 cel pA+ A 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8687 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapAlnRep2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellPapAlnRep1 MCF7 cel pA+ A 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000175 175 GSM765388 Gingeras CSHL LID8686 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellPapAlnRep1 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaAlnRep2 MCF7 cel pA- A 2 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8825 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaAlnRep2 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaAlnRep1 MCF7 cel pA- A 1 MCF-7 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000183 183 GSM767851 Gingeras CSHL LID8824 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaAlnRep1 Alignments mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch MCF-7 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapAlnRep2 IMR90 nuc pA+ A 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 Gingeras CSHL LID45635 nucleus 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90NucleusPapAlnRep1 IMR90 nuc pA+ A 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002628 2628 Gingeras CSHL LID45613 nucleus 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90NucleusPapAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapAlnRep2 IMR90 cyt pA+ A 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002626 2626 Gingeras CSHL LID45612 cytosol 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CytosolPapAlnRep1 IMR90 cyt pA+ A 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002626 2626 Gingeras CSHL LID45611 cytosol 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CytosolPapAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalAlnRep2 IMR90 cel tot A 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-17 wgEncodeEH002623 2623 Gingeras CSHL LID45239 cell 2x101D 2 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 whole cell total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellTotalAlnRep1 IMR90 cel tot A 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-11-16 wgEncodeEH002623 2623 Gingeras CSHL LID45238 cell 2x101D 1 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellTotalAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 whole cell total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapAlnRep2 IMR90 cel pA+ A 2 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 Gingeras CSHL LID45017 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapAlnRep2 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqImr90CellPapAlnRep1 IMR90 cel pA+ A 1 IMR90 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002629 2629 Gingeras CSHL LID45016 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqImr90CellPapAlnRep1 Alignments fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch IMR90 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapAlnRep4 HUVEC nuc pA+ A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8691 nucleus 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapAlnRep4 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusPapAlnRep3 HUVEC nuc pA+ A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000157 157 GSM758565 Gingeras CSHL LID8690 nucleus 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusPapAlnRep3 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaAlnRep4 HUVEC nuc pA- A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9207 nucleus 2x76D 4 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaAlnRep4 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaAlnRep3 HUVEC nuc pA- A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000189 189 GSM767857 Gingeras CSHL LID9206 nucleus 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecNucleusLongnonpolyaAlnRep3 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapAlnRep4 HUVEC cyt pA+ A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8689 cytosol 2x76D 4 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapAlnRep4 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolPapAlnRep3 HUVEC cyt pA+ A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000156 156 GSM758569 Gingeras CSHL LID8688 cytosol 2x76D 3 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolPapAlnRep3 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaAlnRep3 HUVEC cyt pA- A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000200 200 GSM767839 Gingeras CSHL LID18556 cytosol 2x76D 3 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCytosolLongnonpolyaAlnRep3 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC cytosol polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapAlnRep2 HUVEC cel pA+ A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8464 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapAlnRep2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellPapAlnRep1 HUVEC cel pA+ A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000155 155 GSM758563 Gingeras CSHL LID8463 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellPapAlnRep1 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaAlnRep2 HUVEC cel pA- A 2 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8789 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaAlnRep2 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaAlnRep1 HUVEC cel pA- A 1 HUVEC RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000188 188 GSM767856 Gingeras CSHL LID8788 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHuvecCellLongnonpolyaAlnRep1 Alignments umbilical vein endothelial cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HUVEC whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapAlnRep2 HeG2 nuc pA+ A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8535 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapAlnRep2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusPapAlnRep1 HeG2 nuc pA+ A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000158 158 GSM758568 Gingeras CSHL LID8534 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusPapAlnRep1 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaAlnRep2 HeG2 nuc pA- A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9203 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaAlnRep2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaAlnRep1 HeG2 nuc pA- A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000192 192 GSM767850 Gingeras CSHL LID9202 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2NucleusLongnonpolyaAlnRep1 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapAlnRep2 HeG2 cyt pA+ A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8472 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapAlnRep2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolPapAlnRep1 HeG2 cyt pA+ A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000161 161 GSM758576 Gingeras CSHL LID8471 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolPapAlnRep1 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaAlnRep2 HeG2 cyt pA- A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18553 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaAlnRep2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 cytosol polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaAlnRep1 HeG2 cyt pA- A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000202 202 GSM767840 Gingeras CSHL LID18552 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CytosolLongnonpolyaAlnRep1 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 cytosol polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapAlnRep2 HeG2 cel pA+ A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16636 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapAlnRep2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellPapAlnRep1 HeG2 cel pA+ A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000160 160 GSM758575 Gingeras CSHL LID16635 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellPapAlnRep1 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaAlnRep2 HeG2 cel pA- A 2 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8793 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaAlnRep2 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaAlnRep1 HeG2 cel pA- A 1 HepG2 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000159 159 GSM758567 Gingeras CSHL LID8792 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHepg2CellLongnonpolyaAlnRep1 Alignments hepatocellular carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HepG2 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapAlnRep2 HeS3 nuc pA+ A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8560 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapAlnRep2 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusPapAlnRep1 HeS3 nuc pA+ A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000172 172 GSM765403 Gingeras CSHL LID8559 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusPapAlnRep1 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaAlnRep2 HeS3 nuc pA- A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9201 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaAlnRep2 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaAlnRep1 HeS3 nuc pA- A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000190 190 GSM767848 Gingeras CSHL LID9200 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3NucleusLongnonpolyaAlnRep1 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapAlnRep2 HeS3 cyt pA+ A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8470 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapAlnRep2 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolPapAlnRep1 HeS3 cyt pA+ A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000171 171 GSM765404 Gingeras CSHL LID8469 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolPapAlnRep1 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaAlnRep2 HeS3 cyt pA- A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000201 201 GSM767838 Gingeras CSHL LID18551 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CytosolLongnonpolyaAlnRep2 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 cytosol polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapAlnRep2 HeS3 cel pA+ A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16634 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapAlnRep2 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellPapAlnRep1 HeS3 cel pA+ A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000173 173 GSM765402 Gingeras CSHL LID16633 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellPapAlnRep1 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaAlnRep2 HeS3 cel pA- A 2 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8791 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaAlnRep2 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaAlnRep1 HeS3 cel pA- A 1 HeLa-S3 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000191 191 GSM767847 Gingeras CSHL LID8790 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqHelas3CellLongnonpolyaAlnRep1 Alignments cervical carcinoma Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch HeLa-S3 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapAlnRep2 CD20 cel pA+ A 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002665 2665 Gingeras CSHL LID44499 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapAlnRep2 Alignments B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch CD20+ whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPapAlnRep1 CD20 cel pA+ A 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002665 2665 Gingeras CSHL LID44498 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPapAlnRep1 Alignments B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch CD20+ whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamAlnRep2 CD20 cel pA- A 2 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-16 wgEncodeEH002666 2666 Gingeras CSHL LID44660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamAlnRep2 Alignments B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch CD20+ whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqCd20CellPamAlnRep1 CD20 cel pA- A 1 CD20+ RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-11-17 wgEncodeEH002666 2666 Gingeras CSHL LID44659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqCd20CellPamAlnRep1 Alignments B cells from donors RO01778 and RO01794, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch CD20+ whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapAlnRep4 A549 nuc pA+ A 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002625 2625 Gingeras CSHL LID45900 nucleus 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapAlnRep4 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549NucleusPapAlnRep3 A549 nuc pA+ A 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-18 2012-05-14 wgEncodeEH002625 2625 Gingeras CSHL LID45899 nucleus 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549NucleusPapAlnRep3 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapAlnRep4 A549 cyt pA+ A 2 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-17 2012-05-14 wgEncodeEH002624 2624 Gingeras CSHL LID45898 cytosol 2x101D 4 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapAlnRep4 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CytosolPapAlnRep3 A549 cyt pA+ A 1 A549 RnaSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-05-14 wgEncodeEH002624 2624 Gingeras CSHL LID45897 cytosol 2x101D 3 longPolyA Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqA549CytosolPapAlnRep3 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 101 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch A549 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapAlnRep2 A549 cel pA+ A 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8964 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapAlnRep2 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch A549 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellPapAlnRep1 A549 cel pA+ A 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000143 143 GSM758564 Gingeras CSHL LID8963 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellPapAlnRep1 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch A549 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaAlnRep2 A549 cel pA- A 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9006 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaAlnRep2 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch A549 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqA549CellLongnonpolyaAlnRep1 A549 cel pA- A 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000184 184 GSM767854 Gingeras CSHL LID9005 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqA549CellLongnonpolyaAlnRep1 Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch A549 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapAlnRep2 K562 nuc pA+ A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8557 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusPapAlnRep1 K562 nuc pA+ A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000174 174 GSM765387 Gingeras CSHL LID8556 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaAlnRep2 K562 nuc pA- A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9196 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaAlnRep1 K562 nuc pA- A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000194 194 GSM767844 Gingeras CSHL LID9195 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleusLongnonpolyaAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalAlnRep4 K562 ncpm tot A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9190 nucleoplasm 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalAlnRep4 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleoplasm total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleoplasmTotalAlnRep3 K562 ncpm tot A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000182 182 GSM765390 Gingeras CSHL LID9189 nucleoplasm 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleoplasmTotalAlnRep3 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory That part of the nuclear content other than the chromosomes or the nucleolus Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleoplasm total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562NucleolusTotalAlnRep4 K562 nlus tot A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000181 181 GSM765393 Gingeras CSHL LID9188 nucleolus 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562NucleolusTotalAlnRep4 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 nucleolus total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapAlnRep2 K562 cyt pA+ A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000140 140 Gingeras CSHL LID8466 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolPapAlnRep1 K562 cyt pA+ A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2009-07-06 2010-04-06 wgEncodeEH000140 140 Gingeras CSHL LID8465 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaAlnRep2 K562 cyt pA- A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18546 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaAlnRep1 K562 cyt pA- A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-24 2011-09-23 wgEncodeEH000193 193 GSM767849 Gingeras CSHL LID18545 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CytosolLongnonpolyaAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalAlnRep4 K562 chrm tot A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9186 chromatin 2x76D 4 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalAlnRep4 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 chromatin total RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562ChromatinTotalAlnRep3 K562 chrm tot A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH000180 180 GSM765392 Gingeras CSHL LID9185 chromatin 2x76D 3 total Illumina_GA2x wgEncodeCshlLongRnaSeqK562ChromatinTotalAlnRep3 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Nuclear DNA and associated proteins Paired 76 nt directed reads Total RNA extract (longer than 200 nt) Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 chromatin total RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapAlnRep2 K562 cel pA+ A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16628 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellPapAlnRep1 K562 cel pA+ A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000163 163 GSM765405 Gingeras CSHL LID16627 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaAlnRep2 K562 cel pA- A 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8660 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqK562CellLongnonpolyaAlnRep1 K562 cel pA- A 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000162 162 GSM758577 Gingeras CSHL LID8659 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqK562CellLongnonpolyaAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch K562 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusPapAlnRep2 H1hSC nuc pA+ A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000152 152 GSM758574 Gingeras CSHL LID8558 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusPapAlnRep2 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaAlnRep2 H1hSC nuc pA- A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000199 199 GSM767841 Gingeras CSHL LID9199 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescNucleusLongnonpolyaAlnRep2 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolPapAlnRep2 H1hSC cyt pA+ A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000151 151 GSM758570 Gingeras CSHL LID8536 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolPapAlnRep2 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaAlnRep2 H1hSC cyt pA- A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000198 198 GSM767842 Gingeras CSHL LID18549 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCytosolLongnonpolyaAlnRep2 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC cytosol polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapAlnRep2 H1hSC cel pA+ A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8462 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapAlnRep2 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellPapAlnRep1 H1hSC cel pA+ A 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000150 150 GSM758566 Gingeras CSHL LID8461 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellPapAlnRep1 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaAlnRep2 H1hSC cel pA- A 2 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8664 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaAlnRep2 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaAlnRep1 H1hSC cel pA- A 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000149 149 GSM758573 Gingeras CSHL LID8663 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqH1hescCellLongnonpolyaAlnRep1 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapAlnRep2 GM78 nuc pA+ A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8533 nucleus 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleus polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusPapAlnRep1 GM78 nuc pA+ A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000170 170 GSM765386 Gingeras CSHL LID8532 nucleus 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusPapAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleus polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaAlnRep2 GM78 nuc pA- A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-12 2011-10-12 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9198 nucleus 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleus polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaAlnRep1 GM78 nuc pA- A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000187 187 GSM767853 Gingeras CSHL LID9197 nucleus 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878NucleusLongnonpolyaAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleus polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalAlnRep4 GM78 nlus tot A 4 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-28 2013-03-28 wgEncodeEH003034 3034 Gingeras CSHL LID47964 nucleolus 2x101D 4 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalAlnRep4 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleolus total RNA-seq Alignments Rep 4 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878NucleolusTotalAlnRep3 GM78 nlus tot A 3 GM12878 RnaSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-29 wgEncodeEH003034 3034 Gingeras CSHL LID47963 nucleolus 2x101D 3 total Illumina_HiSeq_2000 wgEncodeCshlLongRnaSeqGm12878NucleolusTotalAlnRep3 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The part of the nucleus where ribosomal RNA is actively transcribed Paired 101 nt directed reads Total RNA extract (longer than 200 nt) Illumina HiSeq 2000 Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 nucleolus total RNA-seq Alignments Rep 3 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapAlnRep2 GM78 cyt pA+ A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8468 cytosol 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolPapAlnRep1 GM78 cyt pA+ A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-10-05 2011-07-05 wgEncodeEH000147 147 GSM758560 Gingeras CSHL LID8467 cytosol 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolPapAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaAlnRep2 GM78 cyt pA- A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18548 cytosol 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaAlnRep1 GM78 cyt pA- A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH000186 186 GSM767852 Gingeras CSHL LID18547 cytosol 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory The fluid between the cells outer membrane and the nucleus Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapAlnRep2 GM78 cel pA+ A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16630 cell 2x76D 2 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 whole cell polyA+ RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellPapAlnRep1 GM78 cel pA+ A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000146 146 GSM758559 Gingeras CSHL LID16629 cell 2x76D 1 longPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellPapAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 whole cell polyA+ RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaAlnRep2 GM78 cel pA- A 2 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8662 cell 2x76D 2 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 whole cell polyA- RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression 
wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaAlnRep1 GM78 cel pA- A 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH000148 148 GSM758572 Gingeras CSHL LID8661 cell 2x76D 1 longNonPolyA Illumina_GA2x wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)- RNA longer than 200 nt Illumina Genome Analyzer IIx Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 whole cell polyA- RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression 
wgEncodeDukeAffyExon Duke Affy Exon GSE15805 Affymetrix Exon Array from ENCODE/Duke Expression Description This track displays human tissue microarray data using Affymetrix Human Exon 1.0 ST expression arrays. This RNA expression track was produced as part of the ENCODE Project. The RNA was extracted from cells that were also analyzed by DNaseI hypersensitivity (Duke DNaseI HS), FAIRE (UNC FAIRE), and ChIP (UTA TFBS). Display Conventions and Configuration In contrast to the hg18 annotation, this track now displays exon array data that has been aggregated to the gene level for those probes that have been linked to genes. Probes not linked to genes are not included. The display for this track shows gene probe location and signal value as grayscale-colored items where higher signal values correspond to darker-colored blocks. Items with scores between 900-1000 have signal values greater than 9 that have been linearly scaled for that particular cell type. Items scoring 400-900 have signal values between 4 and 9, and the signal is simply multiplied by 100 to get the score. Items with scores between 200-400 have signal values below 4 that have been linearly scaled to fit that score range. The subtracks within this composite annotation track correspond to data from different cell types and tissues. The configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For information regarding specific microarray probes, turn on the Affy Exon Probes track, which can be found in the Expression track group. See Methods for a description as to how probe level data was processed to produce gene level annotations. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Data from these tracks are stored as bed files whose first six fields follow the bed file standard. The three additional fields are as follows: signalValue: The normalized expression value for a gene, calculated as described below. exonCount: The number of exons used in the calculation of the expression value. constitutiveExons: The number of constitutive exons used in the calculation of the expression value. Methods Cells were grown according to the approved ENCODE cell culture protocols. Total RNA was isolated from these cells using trizol extraction followed by cleanup on RNEasy column (Qiagen) that included a DNaseI step. The RNA was checked for quality using a nanodrop and an Agilent Bioanalyzer. RNA (1 µg) deemed to be of good quality was then processed either by 1) the standard Affymetrix Whole transcript Sense Target labeling protocol that included a riboreduction step, or 2) the NuGEN labeling system. The fragmented biotin-labeled cDNA was hybridized over 16 h to Affymetrix Exon 1.0 ST arrays and scanned on an Affymetrix Scanner 3000 7G using AGCC software. Data from all replicates were then normalized together. Probesets flagged as cross-hybridizing were removed from the analysis (Salomonis et al. 2010). Though these arrays provide exon-level resolution, gene-level expression was estimated by grouping probesets by gene for normalization (Bemmo et al. 2008). Probesets were assigned to genes based on the GENCODE v10 annotation (July 2011). An exon was classified as constitutive or non-constitutive based on whether it was present in all protein-coding transcripts. For genes with at least 4 constitutive probes, only constitutive probesets were used to estimate gene expression. For all other genes, including all non-protein-coding genes, all (non-cross-hybridizing) probesets that mapped to an expressed exon in any transcript of the gene were used. Gene-level expression estimates were normalized using Affymetrix Power Tools (APT) (Lockstone 2011) with the chipstream command "rma-bg, med-norm, pm-gcbg, med-polish". This chipstream calls for an RMA normalization with gc-background correction using antigenomic background probes. While the data was generated using the same microarray platform, two different experimental backgrounds were present due to a change in labeling reagents (Affymetrix vs. NuGEN; see Methods above). It was found that batch effects related to this change were causing array data to group by experimental protocol rather than cell type relatedness. We used an R script (ComBat) to correct for this batch effect (Johnson et al. 2007). Verification When biological replicates were available, data were verified by analyzing replicates displaying a Pearson correlation coefficient > 0.9. Release Notes This is release 3 of this track (April 2012). Several new cell types have been added. The name of cell line Astrocy was changed to NH-A. Credits RNA was extracted from each cell type by Greg Crawford's group at Duke University. RNA was purified and hybridized to Affymetrix Exon arrays by Sridar Chittur and Scott Tenenbaum at the University of Albany-SUNY. Data analyses were primarily performed by Nathan Sheffield (Duke University) with assistance from Melissa Cline (UCSC), Zhancheng Zhang (UNC Chapel Hill), and Darin London (Duke University). Contact: Terry Furey References Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J. Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics. 2008 Nov 7;9:529. Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007 Jan;8(1):118-27. Lockstone HE. Exon array data analysis using Affymetrix power tools and R statistical software. Brief Bioinform. 2011 Nov;12(6):634-44. Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS et al. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10514-9. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeExonArraySuper ENC Exon Array ENCODE Exon Array Expression Description These tracks display microarray data. Samples are hybridized to the Affymetrix Human Exon 1.0 GeneChip. In contrast to traditional microarrays, which are designed to measure overall gene expression, the Affymetrix exon arrays contain separate probesets for each exon. This allows large-scale measurement of alternative splicing, alternative polyadenylation, and alternative promoter usage. Additionally, analysis of the constitutive exons (those included in all transcripts) offer accurate measurement of overall gene expression levels. Further information on the design and content of exon arrays can be found here. Display Conventions Items on these tracks pertain to Affymetrix exon array probesets. For information regarding specific microarray probesets, turn on the Affy Exon Array track, which can be found in the "Expression" track group. These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J. Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics. 2008 Nov 7;9:529. Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, Schweitzer A, Awad T, Sugnet C, Dee S, Davies C, Williams A, Turpaz Y. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics. 2006 Dec 27;7:325. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeDukeAffyExonUrothelSimpleSignalRep2 Urothelia 2 Urothelia AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001076 1076 GSM993598 Crawford Duke 2.0 2 wgEncodeDukeAffyExonUrothelSimpleSignalRep2 None SimpleSignal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Urothelia Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonUrothelSimpleSignalRep1V2 Urothelia 1 Urothelia AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001076 1076 GSM993597 Crawford Duke 2.0 1 wgEncodeDukeAffyExonUrothelSimpleSignalRep1V2 None SimpleSignal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Urothelia Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonUrothelUt189SimpleSignalRep2 Uro UT189 2 Urothelia AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001077 1077 GSM993600 Crawford Duke 2.0 2 wgEncodeDukeAffyExonUrothelUt189SimpleSignalRep2 UT189 SimpleSignal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene Affymetrix Exon Microarray Crawford Crawford - Duke University UT189 E.Coli treatment 1 hour, followed by 24 hour incubation Simple Signal Urothelia UT189 E. coli Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonUrothelUt189SimpleSignalRep1V2 Uro UT189 1 Urothelia AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001077 1077 GSM993599 Crawford Duke 2.0 1 wgEncodeDukeAffyExonUrothelUt189SimpleSignalRep1V2 UT189 SimpleSignal primary ureter cell culture of urothelial cells derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large T antigen gene Affymetrix Exon Microarray Crawford Crawford - Duke University UT189 E.Coli treatment 1 hour, followed by 24 hour incubation Simple Signal Urothelia UT189 E. coli Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonUch1SimpleSignalRep2 UCH-1 2 UCH-1 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002700 2700 GSM993603 Crawford Duke 2.0 2 wgEncodeDukeAffyExonUch1SimpleSignalRep2 None SimpleSignal chordoma cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal UCH-1 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonUch1SimpleSignalRep1 UCH-1 1 UCH-1 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002700 2700 GSM993602 Crawford Duke 2.0 1 wgEncodeDukeAffyExonUch1SimpleSignalRep1 None SimpleSignal chordoma cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal UCH-1 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonStellateSimpleSignalRep2 Stellate 2 Stellate AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001075 1075 GSM993596 Crawford Duke 2.0 2 wgEncodeDukeAffyExonStellateSimpleSignalRep2 None SimpleSignal hepatic stellate cells, liver that was perfused with collagenase and sellected for hepatic stellate cells by density gradient Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Stellate Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonStellateSimpleSignalRep1V2 Stellate 1 Stellate AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001075 1075 GSM993595 Crawford Duke 2.0 1 wgEncodeDukeAffyExonStellateSimpleSignalRep1V2 None SimpleSignal hepatic stellate cells, liver that was perfused with collagenase and sellected for hepatic stellate cells by density gradient Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Stellate Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonProgfibSimpleSignalRep2V2 ProgFib 2 ProgFib AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000241 241 GSM993594 Crawford Duke 2.0 2 wgEncodeDukeAffyExonProgfibSimpleSignalRep2V2 None SimpleSignal fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal ProgFib Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonProgfibSimpleSignalRep1V2 ProgFib 1 ProgFib AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000241 241 GSM993593 Crawford Duke 2.0 1 wgEncodeDukeAffyExonProgfibSimpleSignalRep1V2 None SimpleSignal fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal ProgFib Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonOsteoSimpleSignalRep3V2 Osteobl 3 Osteobl AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000240 240 GSM993592 Crawford Duke 2.0 3 wgEncodeDukeAffyExonOsteoSimpleSignalRep3V2 None SimpleSignal osteoblasts (NHOst) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Osteobl Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonOsteoSimpleSignalRep2V2 Osteobl 2 Osteobl AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000240 240 GSM993591 Crawford Duke 2.0 2 wgEncodeDukeAffyExonOsteoSimpleSignalRep2V2 None SimpleSignal osteoblasts (NHOst) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Osteobl Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonOsteoSimpleSignalRep1V2 Osteobl 1 Osteobl AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000240 240 GSM993590 Crawford Duke 2.0 1 wgEncodeDukeAffyExonOsteoSimpleSignalRep1V2 None SimpleSignal osteoblasts (NHOst) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Osteobl Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonNhekSimpleSignalRep2V2 NHEK 2 NHEK AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000239 239 GSM993589 Crawford Duke 2.0 2 F wgEncodeDukeAffyExonNhekSimpleSignalRep2V2 None SimpleSignal epidermal keratinocytes Affymetrix Exon Microarray Crawford Crawford - Duke University Female Simple Signal NHEK Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonNhekSimpleSignalRep1V2 NHEK 1 NHEK AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000239 239 GSM993588 Crawford Duke 2.0 1 F wgEncodeDukeAffyExonNhekSimpleSignalRep1V2 None SimpleSignal epidermal keratinocytes Affymetrix Exon Microarray Crawford Crawford - Duke University Female Simple Signal NHEK Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonNhaSimpleSignalRep2V2 NH-A 2 NH-A AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000214 214 GSM993460 Crawford Duke 2.0 2 wgEncodeDukeAffyExonNhaSimpleSignalRep2V2 None SimpleSignal astrocytes (also called Astrocy) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal NH-A Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonNhaSimpleSignalRep1V2 NH-A 1 NH-A AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000214 214 GSM993459 Crawford Duke 2.0 1 wgEncodeDukeAffyExonNhaSimpleSignalRep1V2 None SimpleSignal astrocytes (also called Astrocy) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal NH-A Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMyometrSimpleSignalRep2V2 Myometr 2 Myometr AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001074 1074 GSM993587 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMyometrSimpleSignalRep2V2 None SimpleSignal myometrial cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Myometr Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMyometrSimpleSignalRep1V2 Myometr 1 Myometr AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001074 1074 GSM993586 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMyometrSimpleSignalRep1V2 None SimpleSignal myometrial cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Myometr Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMelanoSimpleSignalRep4V2 Melano 4 Melano AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001073 1073 GSM993585 Crawford Duke 2.0 4 wgEncodeDukeAffyExonMelanoSimpleSignalRep4V2 None SimpleSignal epidermal melanocytes Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Melano Exon array Signal Rep 4 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMelanoSimpleSignalRep3V2 Melano 3 Melano AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001073 1073 GSM993584 Crawford Duke 2.0 3 wgEncodeDukeAffyExonMelanoSimpleSignalRep3V2 None SimpleSignal epidermal melanocytes Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Melano Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMelanoSimpleSignalRep2V2 Melano 2 Melano AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001073 1073 GSM993583 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMelanoSimpleSignalRep2V2 None SimpleSignal epidermal melanocytes Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Melano Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMelanoSimpleSignalRep1V2 Melano 1 Melano AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001073 1073 GSM993582 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMelanoSimpleSignalRep1V2 None SimpleSignal epidermal melanocytes Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Melano Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMel2183SimpleSignalRep2 Mel_2183 2 Mel_2183 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002699 2699 GSM993581 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMel2183SimpleSignalRep2 None SimpleSignal Melanoma Cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Mel 2183 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMel2183SimpleSignalRep1 Mel_2183 1 Mel_2183 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002699 2699 GSM993580 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMel2183SimpleSignalRep1 None SimpleSignal Melanoma Cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Mel 2183 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMedulloSimpleSignalRep3V2 Medullo 3 Medullo AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000238 238 GSM993579 Crawford Duke 2.0 3 wgEncodeDukeAffyExonMedulloSimpleSignalRep3V2 None SimpleSignal medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Medullo Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMedulloSimpleSignalRep2V2 Medullo 2 Medullo AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000238 238 GSM993578 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMedulloSimpleSignalRep2V2 None SimpleSignal medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Medullo Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMedulloSimpleSignalRep1V2 Medullo 1 Medullo AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000238 238 GSM993577 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMedulloSimpleSignalRep1V2 None SimpleSignal medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Medullo Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonLncapSimpleSignalRep2V2 LNCaP 2 LNCaP AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000233 233 GSM993565 Crawford Duke 2.0 2 wgEncodeDukeAffyExonLncapSimpleSignalRep2V2 None SimpleSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal LNCaP Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonLncapSimpleSignalRep1V2 LNCaP 1 LNCaP AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000233 233 GSM993564 Crawford Duke 2.0 1 wgEncodeDukeAffyExonLncapSimpleSignalRep1V2 None SimpleSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal LNCaP Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonLncapAndroSimpleSignalRep2V2 LNCaP ANDRO 2 LNCaP AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000234 234 GSM993563 Crawford Duke 2.0 2 wgEncodeDukeAffyExonLncapAndroSimpleSignalRep2V2 androgen SimpleSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Affymetrix Exon Microarray Crawford Crawford - Duke University 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Simple Signal LNCaP Methyltrienolone Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonLncapAndroSimpleSignalRep1V2 LNCaP ANDRO 1 LNCaP AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000234 234 GSM993562 Crawford Duke 2.0 1 wgEncodeDukeAffyExonLncapAndroSimpleSignalRep1V2 androgen SimpleSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Affymetrix Exon Microarray Crawford Crawford - Duke University 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Simple Signal LNCaP Methyltrienolone Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonIpsnihi7SimpleSignalRep2 iPS_NIHi7 2 iPS_NIHi7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002703 2703 GSM993550 Crawford Duke 2.0 2 wgEncodeDukeAffyExonIpsnihi7SimpleSignalRep2 None SimpleSignal iPS cells derived from AG08395 fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal iPS (NIHi7) Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonIpsnihi7SimpleSignalRep1 iPS_NIHi7 1 iPS_NIHi7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002703 2703 GSM993549 Crawford Duke 2.0 1 wgEncodeDukeAffyExonIpsnihi7SimpleSignalRep1 None SimpleSignal iPS cells derived from AG08395 fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal iPS (NIHi7) Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonIpsnihi11SimpleSignalRep2 iPS_NIHi11 2 iPS_NIHi11 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002702 2702 GSM993548 Crawford Duke 2.0 2 wgEncodeDukeAffyExonIpsnihi11SimpleSignalRep2 None SimpleSignal iPS cells derived from AG20443 fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal iPS (NIHi11) Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonIpsnihi11SimpleSignalRep1 iPS_NIHi11 1 iPS_NIHi11 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002702 2702 GSM993547 Crawford Duke 2.0 1 wgEncodeDukeAffyExonIpsnihi11SimpleSignalRep1 None SimpleSignal iPS cells derived from AG20443 fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal iPS (NIHi11) Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonIpscwru1SimpleSignalRep2 iPS_CWRU1 2 iPS_CWRU1 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002701 2701 GSM993546 Crawford Duke 2.0 2 wgEncodeDukeAffyExonIpscwru1SimpleSignalRep2 None SimpleSignal iPS cells derived from MSC658 fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal iPS (CWRU1) Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonIpscwru1SimpleSignalRep1 iPS_CWRU1 1 iPS_CWRU1 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002701 2701 GSM993545 Crawford Duke 2.0 1 wgEncodeDukeAffyExonIpscwru1SimpleSignalRep1 None SimpleSignal iPS cells derived from MSC658 fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal iPS (CWRU1) Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHuh75SimpleSignalRep2 Huh-7.5 2 Huh-7.5 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001071 1071 GSM993542 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHuh75SimpleSignalRep2 None SimpleSignal hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Huh-7.5 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHuh75SimpleSignalRep1V2 Huh-7.5 1 Huh-7.5 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001071 1071 GSM993541 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHuh75SimpleSignalRep1V2 None SimpleSignal hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Huh-7.5 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHuh7SimpleSignalRep2 Huh-7 2 Huh-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001070 1070 GSM993540 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHuh7SimpleSignalRep2 None SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Huh-7 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHuh7SimpleSignalRep1V2 Huh-7 1 Huh-7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001070 1070 GSM993539 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHuh7SimpleSignalRep1V2 None SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Huh-7 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHtr8SimpleSignalRep2V2 HTR8svn 2 HTR8svn AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001068 1068 GSM993538 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHtr8SimpleSignalRep2V2 None SimpleSignal trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HTR8svn Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHtr8SimpleSignalRep1V2 HTR8svn 1 HTR8svn AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001068 1068 GSM993537 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHtr8SimpleSignalRep1V2 None SimpleSignal trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HTR8svn Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmtubefshdSimpleSignalRep3 HSMMtube_FSHD 3 HSMMtube_FSHD AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002694 2694 GSM993536 Crawford Duke 2.0 3 wgEncodeDukeAffyExonHsmmtubefshdSimpleSignalRep3 None SimpleSignal myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMMtube_FSHD Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmtubefshdSimpleSignalRep2 HSMMtube_FSHD 2 HSMMtube_FSHD AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002694 2694 GSM993535 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHsmmtubefshdSimpleSignalRep2 None SimpleSignal myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMMtube_FSHD Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmtubefshdSimpleSignalRep1 HSMMtube_FSHD 1 HSMMtube_FSHD AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002694 2694 GSM993534 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHsmmtubefshdSimpleSignalRep1 None SimpleSignal myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMMtube_FSHD Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmtSimpleSignalRep3V2 HSMMtube 3 HSMMtube AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001067 1067 GSM993533 Crawford Duke 2.0 3 wgEncodeDukeAffyExonHsmmtSimpleSignalRep3V2 None SimpleSignal skeletal muscle myotubes differentiated from the HSMM cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMMtube Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmtSimpleSignalRep2V2 HSMMtube 2 HSMMtube AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001067 1067 GSM993532 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHsmmtSimpleSignalRep2V2 None SimpleSignal skeletal muscle myotubes differentiated from the HSMM cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMMtube Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmtSimpleSignalRep1V2 HSMMtube 1 HSMMtube AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001067 1067 GSM993531 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHsmmtSimpleSignalRep1V2 None SimpleSignal skeletal muscle myotubes differentiated from the HSMM cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMMtube Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmfshdSimpleSignalRep3 HSMM_FSHD 3 HSMM_FSHD AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002693 2693 GSM993530 Crawford Duke 2.0 3 wgEncodeDukeAffyExonHsmmfshdSimpleSignalRep3 None SimpleSignal primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMM_FSHD Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmfshdSimpleSignalRep2 HSMM_FSHD 2 HSMM_FSHD AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002693 2693 GSM993529 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHsmmfshdSimpleSignalRep2 None SimpleSignal primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMM_FSHD Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmfshdSimpleSignalRep1 HSMM_FSHD 1 HSMM_FSHD AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002693 2693 GSM993528 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHsmmfshdSimpleSignalRep1 None SimpleSignal primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMM_FSHD Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmSimpleSignalRep3V2 HSMM 3 HSMM AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001066 1066 GSM993527 Crawford Duke 2.0 3 wgEncodeDukeAffyExonHsmmSimpleSignalRep3V2 None SimpleSignal skeletal muscle myoblasts Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMM Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmSimpleSignalRep2V2 HSMM 2 HSMM AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001066 1066 GSM993526 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHsmmSimpleSignalRep2V2 None SimpleSignal skeletal muscle myoblasts Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMM Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHsmmSimpleSignalRep1V2 HSMM 1 HSMM AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001066 1066 GSM993525 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHsmmSimpleSignalRep1V2 None SimpleSignal skeletal muscle myoblasts Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HSMM Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHpde6e6e7SimpleSignalRep2V2 HPDE6-E6E7 2 HPDE6-E6E7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001065 1065 GSM993524 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHpde6e6e7SimpleSignalRep2V2 None SimpleSignal pancreatic duct cells immortalized with E6E7 gene of HPV Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HPDE6-E6E7 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHpde6e6e7SimpleSignalRep1V2 HPDE6-E6E7 1 HPDE6-E6E7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001065 1065 GSM993523 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHpde6e6e7SimpleSignalRep1V2 None SimpleSignal pancreatic duct cells immortalized with E6E7 gene of HPV Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HPDE6-E6E7 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHmecSimpleSignalRep2V2 HMEC 2 HMEC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000225 225 GSM993522 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHmecSimpleSignalRep2V2 None SimpleSignal mammary epithelial cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HMEC Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHmecSimpleSignalRep1V2 HMEC 1 HMEC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000225 225 GSM993521 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHmecSimpleSignalRep1V2 None SimpleSignal mammary epithelial cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HMEC Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHepatoSimpleSignalRep2V2 Hepatocytes 2 Hepatocytes AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001069 1069 GSM993517 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHepatoSimpleSignalRep2V2 None SimpleSignal primary hepatocytes, liver perfused by enzymes to generate single cell suspension Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Hepatocytes Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHepatoSimpleSignalRep1V2 Hepatocytes 1 Hepatocytes AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001069 1069 GSM993516 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHepatoSimpleSignalRep1V2 None SimpleSignal primary hepatocytes, liver perfused by enzymes to generate single cell suspension Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Hepatocytes Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHek293tSimpleSignalRep2 HEK293T 2 HEK293T AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002692 2692 GSM993508 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHek293tSimpleSignalRep2 None SimpleSignal embryonic kidney that expresses SV40 large T antigen, HEK293 (ATCC number CRL-1573) is the parental cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HEK293T Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHek293tSimpleSignalRep1 HEK293T 1 HEK293T AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002692 2692 GSM993507 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHek293tSimpleSignalRep1 None SimpleSignal embryonic kidney that expresses SV40 large T antigen, HEK293 (ATCC number CRL-1573) is the parental cell line Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HEK293T Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH9esSimpleSignalRep3 H9ES 3 H9ES AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001064 1064 GSM993506 Crawford Duke 2.0 3 wgEncodeDukeAffyExonH9esSimpleSignalRep3 None SimpleSignal embryonic stem cell (hESC) H9 Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H9ES Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH9esSimpleSignalRep2 H9ES 2 H9ES AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001064 1064 GSM993505 Crawford Duke 2.0 2 wgEncodeDukeAffyExonH9esSimpleSignalRep2 None SimpleSignal embryonic stem cell (hESC) H9 Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H9ES Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH9esSimpleSignalRep1V2 H9ES 1 H9ES AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001064 1064 GSM993504 Crawford Duke 2.0 1 wgEncodeDukeAffyExonH9esSimpleSignalRep1V2 None SimpleSignal embryonic stem cell (hESC) H9 Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H9ES Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH7esSimpleSignalRep3 H7-hESC 3 H7-hESC AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002691 2691 GSM993503 Crawford Duke 2.0 3 wgEncodeDukeAffyExonH7esSimpleSignalRep3 None SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H7-hESC Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH7esSimpleSignalRep2 H7-hESC 2 H7-hESC AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002691 2691 GSM993502 Crawford Duke 2.0 2 wgEncodeDukeAffyExonH7esSimpleSignalRep2 None SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H7-hESC Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH7esSimpleSignalRep1 H7-hESC 1 H7-hESC AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002691 2691 GSM993501 Crawford Duke 2.0 1 wgEncodeDukeAffyExonH7esSimpleSignalRep1 None SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H7-hESC Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm19240SimpleSignalRep2V2 GM19240 2 GM19240 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000223 223 GSM993496 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm19240SimpleSignalRep2V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM19240 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm19240SimpleSignalRep1V2 GM19240 1 GM19240 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000223 223 GSM993495 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm19240SimpleSignalRep1V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM19240 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm19239SimpleSignalRep2V2 GM19239 2 GM19239 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000222 222 GSM993494 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm19239SimpleSignalRep2V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM19239 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm19239SimpleSignalRep1V2 GM19239 1 GM19239 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000222 222 GSM993493 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm19239SimpleSignalRep1V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM19239 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm19238SimpleSignalRep2V2 GM19238 2 GM19238 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000221 221 GSM993492 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm19238SimpleSignalRep2V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM19238 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm19238SimpleSignalRep1V2 GM19238 1 GM19238 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000221 221 GSM993491 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm19238SimpleSignalRep1V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM19238 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm18507SimpleSignalRep3V2 GM18507 3 GM18507 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000220 220 GSM993490 Crawford Duke 2.0 3 wgEncodeDukeAffyExonGm18507SimpleSignalRep3V2 None SimpleSignal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM18507 Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm18507SimpleSignalRep2V2 GM18507 2 GM18507 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000220 220 GSM993489 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm18507SimpleSignalRep2V2 None SimpleSignal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM18507 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm18507SimpleSignalRep1V2 GM18507 1 GM18507 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000220 220 GSM993488 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm18507SimpleSignalRep1V2 None SimpleSignal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM18507 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12892SimpleSignalRep2V2 GM12892 2 GM12892 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000219 219 GSM993487 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm12892SimpleSignalRep2V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12892 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12892SimpleSignalRep1V2 GM12892 1 GM12892 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000219 219 GSM993486 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm12892SimpleSignalRep1V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12892 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12891SimpleSignalRep2V2 GM12891 2 GM12891 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000218 218 GSM993485 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm12891SimpleSignalRep2V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12891 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12891SimpleSignalRep1V2 GM12891 1 GM12891 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000218 218 GSM993484 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm12891SimpleSignalRep1V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12891 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGlioblaSimpleSignalRep4V2 Gliobla 4 Gliobla AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000224 224 GSM993480 Crawford Duke 2.0 4 wgEncodeDukeAffyExonGlioblaSimpleSignalRep4V2 None SimpleSignal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Gliobla Exon array Signal Rep 4 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGlioblaSimpleSignalRep3V2 Gliobla 3 Gliobla AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000224 224 GSM993479 Crawford Duke 2.0 3 wgEncodeDukeAffyExonGlioblaSimpleSignalRep3V2 None SimpleSignal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Gliobla Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGlioblaSimpleSignalRep2V2 Gliobla 2 Gliobla AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000224 224 GSM993478 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGlioblaSimpleSignalRep2V2 None SimpleSignal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Gliobla Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGlioblaSimpleSignalRep1V2 Gliobla 1 Gliobla AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000224 224 GSM993477 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGlioblaSimpleSignalRep1V2 None SimpleSignal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Gliobla Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag20443SimpleSignalRep3 FibroP_AG20443 3 FibroP_AG20443 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002706 2706 GSM993476 Crawford Duke 2.0 3 wgEncodeDukeAffyExonFibropag20443SimpleSignalRep3 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG20443) Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag20443SimpleSignalRep2 FibroP_AG20443 2 FibroP_AG20443 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002706 2706 GSM993475 Crawford Duke 2.0 2 wgEncodeDukeAffyExonFibropag20443SimpleSignalRep2 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG20443) Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag20443SimpleSignalRep1 FibroP_AG20443 1 FibroP_AG20443 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002706 2706 GSM993474 Crawford Duke 2.0 1 wgEncodeDukeAffyExonFibropag20443SimpleSignalRep1 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG20443) Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag08396SimpleSignalRep3 FibroP_AG08396 3 FibroP_AG08396 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002705 2705 GSM993473 Crawford Duke 2.0 3 wgEncodeDukeAffyExonFibropag08396SimpleSignalRep3 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG08396) Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag08396SimpleSignalRep2 FibroP_AG08396 2 FibroP_AG08396 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002705 2705 GSM993472 Crawford Duke 2.0 2 wgEncodeDukeAffyExonFibropag08396SimpleSignalRep2 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG08396) Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag08396SimpleSignalRep1 FibroP_AG08396 1 FibroP_AG08396 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002705 2705 GSM993471 Crawford Duke 2.0 1 wgEncodeDukeAffyExonFibropag08396SimpleSignalRep1 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG08396) Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag08395SimpleSignalRep3 FibroP_AG08395 3 FibroP_AG08395 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002704 2704 GSM993470 Crawford Duke 2.0 3 wgEncodeDukeAffyExonFibropag08395SimpleSignalRep3 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG08395) Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag08395SimpleSignalRep2 FibroP_AG08395 2 FibroP_AG08395 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002704 2704 GSM993469 Crawford Duke 2.0 2 wgEncodeDukeAffyExonFibropag08395SimpleSignalRep2 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG08395) Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibropag08395SimpleSignalRep1 FibroP_AG08395 1 FibroP_AG08395 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002704 2704 GSM993468 Crawford Duke 2.0 1 wgEncodeDukeAffyExonFibropag08395SimpleSignalRep1 None SimpleSignal fibroblasts taken from individuals with Parkinson's disease Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal FibroP (AG08395) Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibroblSimpleSignalRep2V2 Fibrobl 2 Fibrobl AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000216 216 GSM993467 Crawford Duke 2.0 2 wgEncodeDukeAffyExonFibroblSimpleSignalRep2V2 None SimpleSignal child fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Fibrobl Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonFibroblSimpleSignalRep1V2 Fibrobl 1 Fibrobl AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000216 216 GSM993466 Crawford Duke 2.0 1 wgEncodeDukeAffyExonFibroblSimpleSignalRep1V2 None SimpleSignal child fibroblast Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Fibrobl Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonColo829SimpleSignalRep2 Colo829 2 Colo829 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002690 2690 GSM993465 Crawford Duke 2.0 2 wgEncodeDukeAffyExonColo829SimpleSignalRep2 None SimpleSignal malignant melanoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Colo829 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonColo829SimpleSignalRep1 Colo829 1 Colo829 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002690 2690 GSM993464 Crawford Duke 2.0 1 wgEncodeDukeAffyExonColo829SimpleSignalRep1 None SimpleSignal malignant melanoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Colo829 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonCllSimpleSignalRep2V2 CLL 2 CLL AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001061 1061 GSM993463 Crawford Duke 2.0 2 wgEncodeDukeAffyExonCllSimpleSignalRep2V2 None SimpleSignal chronic lymphocytic leukemia cell, T-cell lymphocyte Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal CLL Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonCllSimpleSignalRep1V2 CLL 1 CLL AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001061 1061 GSM993462 Crawford Duke 2.0 1 wgEncodeDukeAffyExonCllSimpleSignalRep1V2 None SimpleSignal chronic lymphocytic leukemia cell, T-cell lymphocyte Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal CLL Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonChorionSimpleSignalRep1V2 Chorion 1 Chorion AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000215 215 GSM993461 Crawford Duke 2.0 1 wgEncodeDukeAffyExonChorionSimpleSignalRep1V2 None SimpleSignal chorion cells (outermost of two fetal membranes), fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes. Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal Chorion Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonAosmcSimpleSignalRep2V2 AoSMC 2 AoSMC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001059 1059 GSM993454 Crawford Duke 2.0 2 wgEncodeDukeAffyExonAosmcSimpleSignalRep2V2 None SimpleSignal aortic smooth muscle cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal AoSMC Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonAosmcSimpleSignalRep1V2 AoSMC 1 AoSMC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001059 1059 GSM993453 Crawford Duke 2.0 1 wgEncodeDukeAffyExonAosmcSimpleSignalRep1V2 None SimpleSignal aortic smooth muscle cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal AoSMC Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonAosmcTgfbSimpleSignalRep2V2 AoSMC TGFb 2 AoSMC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001060 1060 GSM993458 Crawford Duke 2.0 2 wgEncodeDukeAffyExonAosmcTgfbSimpleSignalRep2V2 TGFb SimpleSignal aortic smooth muscle cells Affymetrix Exon Microarray Crawford Crawford - Duke University 1 ng/mL transforming growth factor beta for 24 hours (Crawford) Simple Signal AoSMC TGFb Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonAosmcTgfbSimpleSignalRep1V2 AoSMC TGFb 1 AoSMC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001060 1060 GSM993457 Crawford Duke 2.0 1 wgEncodeDukeAffyExonAosmcTgfbSimpleSignalRep1V2 TGFb SimpleSignal aortic smooth muscle cells Affymetrix Exon Microarray Crawford Crawford - Duke University 1 ng/mL transforming growth factor beta for 24 hours (Crawford) Simple Signal AoSMC TGFb Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonAosmcSerumfreeSimpleSignalRep2V2 AoSMC 2 AoSMC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001058 1058 GSM993456 Crawford Duke 2.0 2 wgEncodeDukeAffyExonAosmcSerumfreeSimpleSignalRep2V2 serum_free_media SimpleSignal aortic smooth muscle cells Affymetrix Exon Microarray Crawford Crawford - Duke University Grown with growth factors, then switched to media that contains no FBS for 36 hours (Crawford) Simple Signal AoSMC Serum-free media Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonAosmcSerumfreeSimpleSignalRep1V2 AoSMC 1 AoSMC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001058 1058 GSM993455 Crawford Duke 2.0 1 wgEncodeDukeAffyExonAosmcSerumfreeSimpleSignalRep1V2 serum_free_media SimpleSignal aortic smooth muscle cells Affymetrix Exon Microarray Crawford Crawford - Duke University Grown with growth factors, then switched to media that contains no FBS for 36 hours (Crawford) Simple Signal AoSMC Serum-free media Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExon8988tSimpleSignalRep2V2 8988T 2 8988T AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001057 1057 GSM993450 Crawford Duke 2.0 2 wgEncodeDukeAffyExon8988tSimpleSignalRep2V2 None SimpleSignal pancreas adenocarcinoma (PA-TU-8988T), "established in 1985 from the liver metastasis of a primary pancreatic adenocarcinoma from a 64-year-old woman" - DSMZ Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal 8988T Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExon8988tSimpleSignalRep1V2 8988T 1 8988T AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001057 1057 GSM993449 Crawford Duke 2.0 1 wgEncodeDukeAffyExon8988tSimpleSignalRep1V2 None SimpleSignal pancreas adenocarcinoma (PA-TU-8988T), "established in 1985 from the liver metastasis of a primary pancreatic adenocarcinoma from a 64-year-old woman" - DSMZ Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal 8988T Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7SimpleSignalRep1V2 MCF-7 1 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000235 235 GSM993601 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMcf7SimpleSignalRep1V2 None SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal MCF-7 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7VehSimpleSignalRep2V2 MCF-7 Veh 2 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000237 237 GSM993576 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMcf7VehSimpleSignalRep2V2 vehicle SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Charcoal stripped hormone-free FBS for 72 hours (Crawford) Simple Signal MCF-7 Vehicle Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7VehSimpleSignalRep1V2 MCF-7 Veh 1 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000237 237 GSM993575 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMcf7VehSimpleSignalRep1V2 vehicle SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Charcoal stripped hormone-free FBS for 72 hours (Crawford) Simple Signal MCF-7 Vehicle Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7RandshrnaSimpleSignalRep3 MCF-7 RANDsh 3 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002698 2698 GSM993574 Crawford Duke 2.0 3 wgEncodeDukeAffyExonMcf7RandshrnaSimpleSignalRep3 Randomized_shRNA_control SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. Simple Signal MCF-7 Randomized shRNA control Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7RandshrnaSimpleSignalRep2 MCF-7 RANDsh 2 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002698 2698 GSM993573 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMcf7RandshrnaSimpleSignalRep2 Randomized_shRNA_control SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. Simple Signal MCF-7 Randomized shRNA control Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7RandshrnaSimpleSignalRep1 MCF-7 RANDsh 1 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002698 2698 GSM993572 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMcf7RandshrnaSimpleSignalRep1 Randomized_shRNA_control SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. Simple Signal MCF-7 Randomized shRNA control Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7HypoxlacSimpleSignalRep1 MCF-7 Hypox 1 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002697 2697 GSM993571 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMcf7HypoxlacSimpleSignalRep1 Hypoxia_LacAcid SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University 24 h with 1% p02 and 10mM Lactate, pH 6.7 (Crawford) Simple Signal MCF-7 Hypoxia, Lactic acidosis Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7EstroSimpleSignalRep2V2 MCF-7 ESTRO 2 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000236 236 GSM993570 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMcf7EstroSimpleSignalRep2V2 estrogen SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University 45 min with 100 nM Estradiol (Crawford) Simple Signal MCF-7 Estradiol 100 nM Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7EstroSimpleSignalRep1V2 MCF-7 ESTRO 1 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000236 236 GSM993569 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMcf7EstroSimpleSignalRep1V2 estrogen SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University 45 min with 100 nM Estradiol (Crawford) Simple Signal MCF-7 Estradiol 100 nM Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7CtcfshrnaSimpleSignalRep3 MCF-7 CTCFsh 3 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002696 2696 GSM993568 Crawford Duke 2.0 3 wgEncodeDukeAffyExonMcf7CtcfshrnaSimpleSignalRep3 CTCF_shRNA_knockdown SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. Simple Signal MCF-7 CTCF shRNA knockdown Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7CtcfshrnaSimpleSignalRep2 MCF-7 CTCFsh 2 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002696 2696 GSM993567 Crawford Duke 2.0 2 wgEncodeDukeAffyExonMcf7CtcfshrnaSimpleSignalRep2 CTCF_shRNA_knockdown SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. Simple Signal MCF-7 CTCF shRNA knockdown Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonMcf7CtcfshrnaSimpleSignalRep1 MCF-7 CTCFsh 1 MCF-7 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002696 2696 GSM993566 Crawford Duke 2.0 1 wgEncodeDukeAffyExonMcf7CtcfshrnaSimpleSignalRep1 CTCF_shRNA_knockdown SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. Simple Signal MCF-7 CTCF shRNA knockdown Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHuvecSimpleSignalRep2V2 HUVEC 2 HUVEC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000226 226 GSM993544 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHuvecSimpleSignalRep2V2 None SimpleSignal umbilical vein endothelial cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HUVEC Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHuvecSimpleSignalRep1V2 HUVEC 1 HUVEC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000226 226 GSM993543 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHuvecSimpleSignalRep1V2 None SimpleSignal umbilical vein endothelial cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HUVEC Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHepg2SimpleSignalRep3V2 HepG2 3 HepG2 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000230 230 GSM993520 Crawford Duke 2.0 3 wgEncodeDukeAffyExonHepg2SimpleSignalRep3V2 None SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HepG2 Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHepg2SimpleSignalRep2V2 HepG2 2 HepG2 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000230 230 GSM993519 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHepg2SimpleSignalRep2V2 None SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HepG2 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHepg2SimpleSignalRep1V2 HepG2 1 HepG2 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000230 230 GSM993518 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHepg2SimpleSignalRep1V2 None SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HepG2 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3SimpleSignalRep3V2 HeLa-S3 3 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000227 227 GSM993511 Crawford Duke 2.0 3 wgEncodeDukeAffyExonHelas3SimpleSignalRep3V2 None SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HeLa-S3 Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3SimpleSignalRep2V2 HeLa-S3 2 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000227 227 GSM993510 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHelas3SimpleSignalRep2V2 None SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HeLa-S3 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3SimpleSignalRep1V2 HeLa-S3 1 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000227 227 GSM993509 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHelas3SimpleSignalRep1V2 None SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal HeLa-S3 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3Ifng4hSimpleSignalRep2V2 HeLa-S3 2 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000229 229 GSM993515 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHelas3Ifng4hSimpleSignalRep2V2 IFNg4h SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Interferon gamma treatment - 4 hours with 5 ng/ml (Crawford) Simple Signal HeLa-S3 IFN-g 4 h Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3Ifng4hSimpleSignalRep1V2 HeLa-S3 1 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000229 229 GSM993514 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHelas3Ifng4hSimpleSignalRep1V2 IFNg4h SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University Interferon gamma treatment - 4 hours with 5 ng/ml (Crawford) Simple Signal HeLa-S3 IFN-g 4 h Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3Ifna4hSimpleSignalRep2V2 HeLa-S3 2 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000228 228 GSM993513 Crawford Duke 2.0 2 wgEncodeDukeAffyExonHelas3Ifna4hSimpleSignalRep2V2 IFNa4h SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University 4 hours of 500 U/ml Interferon alpha (Crawford) Simple Signal HeLa-S3 IFN-a 4 h Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonHelas3Ifna4hSimpleSignalRep1V2 HeLa-S3 1 HeLa-S3 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000228 228 GSM993512 Crawford Duke 2.0 1 wgEncodeDukeAffyExonHelas3Ifna4hSimpleSignalRep1V2 IFNa4h SimpleSignal cervical carcinoma Affymetrix Exon Microarray Crawford Crawford - Duke University 4 hours of 500 U/ml Interferon alpha (Crawford) Simple Signal HeLa-S3 IFN-a 4 h Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonA549SimpleSignalRep2 A549 2 A549 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002689 2689 GSM993452 Crawford Duke 2.0 2 wgEncodeDukeAffyExonA549SimpleSignalRep2 None SimpleSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal A549 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonA549SimpleSignalRep1 A549 1 A549 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002689 2689 GSM993451 Crawford Duke 2.0 1 wgEncodeDukeAffyExonA549SimpleSignalRep1 None SimpleSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal A549 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562SimpleSignalRep4 K562 4 K562 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH001072 1072 GSM993557 Crawford Duke 2.0 4 wgEncodeDukeAffyExonK562SimpleSignalRep4 None SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal K562 Exon array Signal Rep 4 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562SimpleSignalRep3V2 K562 3 K562 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001072 1072 GSM993556 Crawford Duke 2.0 3 wgEncodeDukeAffyExonK562SimpleSignalRep3V2 None SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal K562 Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562SimpleSignalRep2V2 K562 2 K562 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001072 1072 GSM993554 Crawford Duke 2.0 2 wgEncodeDukeAffyExonK562SimpleSignalRep2V2 None SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal K562 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562SimpleSignalRep1V2 K562 1 K562 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001072 1072 GSM993552 Crawford Duke 2.0 1 wgEncodeDukeAffyExonK562SimpleSignalRep1V2 None SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal K562 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562NabutSimpleSignalRep4 K562 Nabut 4 K562 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002695 2695 GSM993561 Crawford Duke 2.0 4 wgEncodeDukeAffyExonK562NabutSimpleSignalRep4 NaBut SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University 0.5 mM Sodium Butyrate for 72 hours Simple Signal K562 NaBut Exon array Signal Rep 4 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562NabutSimpleSignalRep3 K562 Nabut 3 K562 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002695 2695 GSM993560 Crawford Duke 2.0 3 wgEncodeDukeAffyExonK562NabutSimpleSignalRep3 NaBut SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University 0.5 mM Sodium Butyrate for 72 hours Simple Signal K562 NaBut Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562NabutSimpleSignalRep2 K562 Nabut 2 K562 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002695 2695 GSM993559 Crawford Duke 2.0 2 wgEncodeDukeAffyExonK562NabutSimpleSignalRep2 NaBut SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University 0.5 mM Sodium Butyrate for 72 hours Simple Signal K562 NaBut Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonK562NabutSimpleSignalRep1 K562 NaBut 1 K562 AffyExonArray ENCODE Mar 2012 Freeze 2012-03-16 2012-12-16 wgEncodeEH002695 2695 GSM993558 Crawford Duke 2.0 1 wgEncodeDukeAffyExonK562NabutSimpleSignalRep1 NaBut SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Crawford Crawford - Duke University 0.5 mM Sodium Butyrate for 72 hours Simple Signal K562 NaBut Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH1hescSimpleSignalRep4V2 H1-hESC 4 H1-hESC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001063 1063 GSM993500 Crawford Duke 2.0 4 wgEncodeDukeAffyExonH1hescSimpleSignalRep4V2 None SimpleSignal embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H1-hESC Exon array Signal Rep 4 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH1hescSimpleSignalRep3V2 H1-hESC 3 H1-hESC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001063 1063 GSM993499 Crawford Duke 2.0 3 wgEncodeDukeAffyExonH1hescSimpleSignalRep3V2 None SimpleSignal embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H1-hESC Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH1hescSimpleSignalRep2V2 H1-hESC 2 H1-hESC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001063 1063 GSM993498 Crawford Duke 2.0 2 wgEncodeDukeAffyExonH1hescSimpleSignalRep2V2 None SimpleSignal embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H1-hESC Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonH1hescSimpleSignalRep1V2 H1-hESC 1 H1-hESC AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH001063 1063 GSM993497 Crawford Duke 2.0 1 wgEncodeDukeAffyExonH1hescSimpleSignalRep1V2 None SimpleSignal embryonic stem cells Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal H1-hESC Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12878SimpleSignalRep3V2 GM12878 3 GM12878 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000217 217 GSM993483 Crawford Duke 2.0 3 wgEncodeDukeAffyExonGm12878SimpleSignalRep3V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12878 Exon array Signal Rep 3 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12878SimpleSignalRep2V2 GM12878 2 GM12878 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000217 217 GSM993482 Crawford Duke 2.0 2 wgEncodeDukeAffyExonGm12878SimpleSignalRep2V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12878 Exon array Signal Rep 2 from ENCODE/Duke Expression 
wgEncodeDukeAffyExonGm12878SimpleSignalRep1V2 GM12878 1 GM12878 AffyExonArray ENCODE Mar 2012 Freeze 2009-12-16 2010-09-16 wgEncodeEH000217 217 GSM993481 Crawford Duke 2.0 1 wgEncodeDukeAffyExonGm12878SimpleSignalRep1V2 None SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Affymetrix Exon Microarray Crawford Crawford - Duke University Simple Signal GM12878 Exon array Signal Rep 1 from ENCODE/Duke Expression 
wgEncodeGisChiaPet GIS ChIA-PET GSE39495 Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan Regulation Description This track was produced as part of the ENCODE Project. It shows the locations of protein factor mediated chromatin interactions determined by Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) data (Fullwood et al., 2010) extracted from five different human cancer cell lines (K562 (chronic myeloid leukemia), HCT116 (colorectal cancer), HeLa-S3 (cervical cancer), MCF-7 (breast cancer), and NB4 (promyelocytic)). A chromatin interaction is defined as the association of two regions of the genome that are far apart in terms of genomic distance, but are spatially proximate to each other in the 3-dimensional cellular nucleus. Additionally, ChIA-PET experiments generate transcription factor binding sites. A binding site is defined as a region of the genome that is highly enriched by specific Chromatin ImmunoPrecipitation (ChIP) against a transcription factor, which indicates that the transcription factor binds specifically to this region. The protein factors displayed in the track include estrogen receptor alpha (ER&#945;), RNA polymerase II (RNAPII), and CCCTC binding factor (CTCF). Display Conventions and Configuration In the graphical display, the PETs are represented by two blocks one for each end. These blocks are connected by a horizontal line if both ends are in the same chromosome. If the two ends are on different chromosomes, only one block will display. PET sequences that overlap at both ends form PET clusters. The number of PETs in a cluster reflects the strength of a chromatin interaction. Singleton PETs (PETs without a cluster) are potentially false positives, whereas PET clusters of more than 3 PETs could indicate genuine chromatin interactions. The density graph of the tags shows the ChIP enrichment at different points of genome, and high peaks indicate transcription factor binding sites. Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Interactions ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. Signal Density graph (wiggle) of signal enrichment based on aligned read density. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a global de novo high-throughput method for characterizing the 3-dimensional structure of chromatin in the nucleus. In the ChIA-PET protocol, samples were cross-linked and fragmented, then subjected to chromatin immunoprecipitation. The DNA fragments that were brought together by the chromatin interactions were then proximity-ligated. During this proximity-ligation step, the half-linkers (created by the fragmentation) containing flanking MmeI sites (type IIS restriction enzymes) were first ligated to the DNA fragments and then ligated to each other to form full linkers. Full linkers bridge either two ends of a self-circularized fragment, or two ends of two different chromatin fragments. The material was then reverse cross-linked, purified and digested with MmeI. MmeI cuts 20 base pairs away from its recognition site. Tag-linker-tag (paired-end tag, PET) constructs were sequenced by ultra-high-throughput methods (Illumina or SOLiD paired-end sequencing). ChIA-PET reads were processed with the ChIA-PET Tool (Li et al., 2010) by the following steps: linker filtering, short reads mapping, PET classification, binding site identification, and interaction cluster identification. The high-confidence binding sites and chromatin interaction clusters were reported. Verification Chromatin interactions identified by ChIA-PET have been validated by 3C, ChIP-3C, 4C and DNA-FISH (Fullwood et al., 2009). Credits Genome Institute of Singapore: Guoliang Li, Xiaoan Ruan, Kuljeet Singh Sandhu, Fabianus Hendriyan Mulawadi, Huay Mei Poh, Yufen Goh, Su Qin Peh, Wing-Kin Sung, Yijun Ruan Stanford University: Raymond Auerbach, Michael Snyder Contact: Yijun Ruan References Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y. Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25. Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009 Nov 5;462(7269):58-64. Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11(2):R22. Publications Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012 Jan 20;148(1-2):84-98. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeChromSuper ENC Chromatin ENCODE Chromatin Interactions Expression Description These tracks display evidence of chromatin interactions in ENCODE cell types. A chromatin interaction is defined as two regions of the genome that are far apart in terms of genomic distance, but are spatially proximate to each other in the 3-dimensional cellular nucleus. Binding sites are also displayed when a transcription factor is used in the assay. A binding site is defined as a region of the genome that is highly enriched by specific Chromatin Immunoprecipitation (ChIP) against a transcription factor, which indicates that the transcription factor binds specifically to this region. ChIA-PET: The Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) (Li 2010, Fullwood 2010) track shows the locations of RNA polymerase II-bound (RNAPII-bound) chromatin interactions determined by Paired-End Tag (PET) sequencing using proximity-ligated chromatin extracts from human cell lines. The RNAPII ChIA-PET experiment generates RNAPII binding sites. Generally, a chromatin interaction is more likely to connect two RNAPII binding sites together. 5C: Chromosome Conformation Capture Carbon Copy (5C) (Dostie 2006) maps genomic interactions of a focused set of restriction enzymes. The three-dimensional organization of chromosomes and chromatin domains is obtained by cross-linking, digestion, ligation and then detection (Dekker 2002). Display Conventions These are multi-view composite tracks that contains multiple data types controllable using the 'Select view' function as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Further details on display conventions and data interpretation are available in the subtrack descriptions. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002 Feb 15;295(5558):1306-11. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 Oct;16(10):1299-309. Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y. Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25. Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11(2):R22. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeGisChiaPetSignal Signal Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetNb4Pol2SigRep1 NB4 Pol2 Sig 1 Pol2 NB4 ChiaPet ENCODE Mar 2012 Freeze 2011-09-24 2012-04-23 wgEncodeEH001431 1431 GSM970214 Ruan GIS-Ruan IHN009M_hg19 1 wgEncodeGisChiaPetNb4Pol2SigRep1 Signal RNA Polymerase II acute promyelocytic leukemia cell line. (PMID: 1995093) Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal NB4 Pol2 ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetHct116Pol2SigRep1 HCT116 Pol2 Sig 1 Pol2 HCT-116 ChiaPet ENCODE Mar 2012 Freeze 2011-09-23 2012-04-23 wgEncodeEH001427 1427 GSM970210 Ruan GIS-Ruan CHH524M 1 wgEncodeGisChiaPetHct116Pol2SigRep1 Signal RNA Polymerase II colorectal carcinoma (PMID: 7214343) Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal HCT-116 Pol2 ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2SigRep4 MCF7 Pol2 Sig 4 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-27 2012-04-23 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM163M_L4 4 wgEncodeGisChiaPetMcf7Pol2SigRep4 Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 Pol2 ChIA-PET Signal Rep 4 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2SigRep3 MCF7 Pol2 Sig 3 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-27 2011-06-08 2012-03-08 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM160M_L4 3 wgEncodeGisChiaPetMcf7Pol2SigRep3 Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 Pol2 ChIA-PET Signal Rep 3 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2SigRep2 MCF7 Pol2 Sig 2 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-23 2012-04-23 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM053T_hg19 2 wgEncodeGisChiaPetMcf7Pol2SigRep2 Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 Pol2 ChIA-PET Signal Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2SigRep1 MCF7 Pol2 Sig 1 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-26 2012-04-23 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM040M_hg19 1 wgEncodeGisChiaPetMcf7Pol2SigRep1 Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 Pol2 ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7EraaSigRep3 MCF7 ERa Sig 3 ERalpha_a MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-24 2012-04-23 wgEncodeEH001429 1429 GSM970212 Ruan GIS-Ruan IHM096M 3 wgEncodeGisChiaPetMcf7EraaSigRep3 Signal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 ERalpha a ChIA-PET Signal Rep 3 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7EraaSigRep2 MCF7 ERa Sig 2 ERalpha_a MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-21 2012-04-21 wgEncodeEH001429 1429 GSM970212 Ruan GIS-Ruan IHH015T_hg19 2 wgEncodeGisChiaPetMcf7EraaSigRep2 Signal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 ERalpha a ChIA-PET Signal Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7EraaSigRep1 MCF7 ERa Sig 1 ERalpha_a MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-20 2012-04-20 wgEncodeEH001429 1429 GSM970212 Ruan GIS-Ruan IHM001T_hg19 1 wgEncodeGisChiaPetMcf7EraaSigRep1 Signal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 ERalpha a ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7CtcfSigRep2 MCF7 CTCF Sig 2 CTCF MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-08-30 2011-06-08 2012-03-08 wgEncodeEH002076 2076 GSM970215 Ruan GIS-Ruan CHM077M 2 wgEncodeGisChiaPetMcf7CtcfSigRep2 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 CTCF ChIA-PET Signal Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7CtcfSigRep1 MCF7 CTCF Sig 1 CTCF MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-08-30 2011-06-08 2012-03-08 wgEncodeEH002076 2076 GSM970215 Ruan GIS-Ruan CHM076M 1 wgEncodeGisChiaPetMcf7CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal MCF-7 CTCF ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetHelas3Pol2SigRep1 HeLaS3 Pol2 Sig 1 Pol2 HeLa-S3 ChiaPet ENCODE Mar 2012 Freeze 2011-09-24 2012-04-23 wgEncodeEH001426 1426 GSM970211 Ruan GIS-Ruan IHH025M_hg19 1 wgEncodeGisChiaPetHelas3Pol2SigRep1 Signal RNA Polymerase II cervical carcinoma Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal HeLa-S3 Pol2 ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetK562Pol2SigRep2 K562 Pol2 Sig 2 Pol2 K562 ChiaPet ENCODE Mar 2012 Freeze 2011-08-19 2011-02-05 2011-11-04 wgEncodeEH001428 1428 GSM970213 Ruan GIS-Ruan CHK019M_L2_lane24 2 wgEncodeGisChiaPetK562Pol2SigRep2 Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal K562 Pol2 ChIA-PET Signal Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetK562Pol2SigRep1 K562 Pol2 Sig 1 Pol2 K562 ChiaPet ENCODE Mar 2012 Freeze 2011-08-23 2011-02-05 2011-11-04 wgEncodeEH001428 1428 GSM970213 Ruan GIS-Ruan CHK019M_L2_lane13 1 wgEncodeGisChiaPetK562Pol2SigRep1 Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal K562 Pol2 ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetK562CtcfSigRep1 K562 CTCF Sig 1 CTCF K562 ChiaPet ENCODE Mar 2012 Freeze 2011-08-30 2011-06-08 2012-03-08 wgEncodeEH002075 2075 GSM970216 Ruan GIS-Ruan CTCF_K562M_L7 1 wgEncodeGisChiaPetK562CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) Signal K562 CTCF ChIA-PET Signal Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetInteractions Interactions Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetNb4Pol2InteractionsRep1 NB4 Pol2 Int 1 Pol2 NB4 ChiaPet ENCODE Mar 2012 Freeze 2011-09-24 2011-01-20 2011-10-20 wgEncodeEH001431 1431 GSM970214 Ruan GIS-Ruan IHN009M_hg19 1 wgEncodeGisChiaPetNb4Pol2InteractionsRep1 Interactions RNA Polymerase II acute promyelocytic leukemia cell line. (PMID: 1995093) Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. NB4 Pol2 ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetHct116Pol2InteractionsRep1 HCT116 Pol2 Int 1 Pol2 HCT-116 ChiaPet ENCODE Mar 2012 Freeze 2011-09-23 2011-01-20 2011-10-20 wgEncodeEH001427 1427 GSM970210 Ruan GIS-Ruan CHH524M 1 wgEncodeGisChiaPetHct116Pol2InteractionsRep1 Interactions RNA Polymerase II colorectal carcinoma (PMID: 7214343) Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. HCT-116 Pol2 ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2InteractionsRep4 MCF7 Pol2 Int 4 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-27 2011-01-20 2011-10-20 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM163M_L4 4 wgEncodeGisChiaPetMcf7Pol2InteractionsRep4 Interactions RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 Pol2 ChIA-PET Interactions Rep 4 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2InteractionsRep3 MCF7 Pol2 Int 3 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-27 2011-06-08 2012-03-08 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM160M_L4 3 wgEncodeGisChiaPetMcf7Pol2InteractionsRep3 Interactions RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 Pol2 ChIA-PET Interactions Rep 3 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2InteractionsRep2 MCF7 Pol2 Int 2 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-23 2011-01-20 2011-10-20 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM053T_hg19 2 wgEncodeGisChiaPetMcf7Pol2InteractionsRep2 Interactions RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 Pol2 ChIA-PET Interactions Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7Pol2InteractionsRep1 MCF7 Pol2 Int 1 Pol2 MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-26 2011-01-20 2011-10-20 wgEncodeEH001430 1430 GSM970209 Ruan GIS-Ruan CHM040M_hg19 1 wgEncodeGisChiaPetMcf7Pol2InteractionsRep1 Interactions RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 Pol2 ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7EraaInteractionsRep3 MCF7 ERa Int 3 ERalpha_a MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-24 2012-04-23 wgEncodeEH001429 1429 GSM970212 Ruan GIS-Ruan IHM096M 3 wgEncodeGisChiaPetMcf7EraaInteractionsRep3 Interactions This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 ERalpha a ChIA-PET Interactions Rep 3 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7EraaInteractionsRep2 MCF7 ERa Int 2 ERalpha_a MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-21 2012-04-21 wgEncodeEH001429 1429 GSM970212 Ruan GIS-Ruan IHH015T_hg19 2 wgEncodeGisChiaPetMcf7EraaInteractionsRep2 Interactions This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 ERalpha a ChIA-PET Interactions Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7EraaInteractionsRep1 MCF7 ERa Int 1 ERalpha_a MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-09-20 2012-04-20 wgEncodeEH001429 1429 GSM970212 Ruan GIS-Ruan IHM001T_hg19 1 wgEncodeGisChiaPetMcf7EraaInteractionsRep1 Interactions This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 ERalpha a ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7CtcfInteractionsRep2 MCF7 CTCF Int 2 CTCF MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-08-30 2011-06-08 2012-03-08 wgEncodeEH002076 2076 GSM970215 Ruan GIS-Ruan CHM077M 2 wgEncodeGisChiaPetMcf7CtcfInteractionsRep2 Interactions CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 CTCF ChIA-PET Interactions Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetMcf7CtcfInteractionsRep1 MCF7 CTCF Int 1 CTCF MCF-7 ChiaPet ENCODE Mar 2012 Freeze 2011-08-30 2011-06-08 2012-03-08 wgEncodeEH002076 2076 GSM970215 Ruan GIS-Ruan CHM076M 1 wgEncodeGisChiaPetMcf7CtcfInteractionsRep1 Interactions CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. MCF-7 CTCF ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetHelas3Pol2InteractionsRep1 HeLaS3 Pol2 Int 1 Pol2 HeLa-S3 ChiaPet ENCODE Mar 2012 Freeze 2011-09-24 2011-01-20 2011-10-20 wgEncodeEH001426 1426 GSM970211 Ruan GIS-Ruan IHH025M_hg19 1 wgEncodeGisChiaPetHelas3Pol2InteractionsRep1 Interactions RNA Polymerase II cervical carcinoma Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. HeLa-S3 Pol2 ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetK562Pol2InteractionsRep2 K562 Pol2 Int 2 Pol2 K562 ChiaPet ENCODE Mar 2012 Freeze 2011-02-05 2011-01-20 2011-10-20 wgEncodeEH001428 1428 GSM970213 Ruan GIS-Ruan CHK019M_L2_lane24 2 wgEncodeGisChiaPetK562Pol2InteractionsRep2 Interactions RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. K562 Pol2 ChIA-PET Interactions Rep 2 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetK562Pol2InteractionsRep1 K562 Pol2 Int 1 Pol2 K562 ChiaPet ENCODE Mar 2012 Freeze 2011-02-05 2011-01-20 2011-10-20 wgEncodeEH001428 1428 GSM970213 Ruan GIS-Ruan CHK019M_L2_lane13 1 wgEncodeGisChiaPetK562Pol2InteractionsRep1 Interactions RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. K562 Pol2 ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisChiaPetK562CtcfInteractionsRep1 K562 CTCF Int 1 CTCF K562 ChiaPet ENCODE Mar 2012 Freeze 2011-08-30 2011-06-08 2012-03-08 wgEncodeEH002075 2075 GSM970216 Ruan GIS-Ruan CTCF_K562M_L7 1 wgEncodeGisChiaPetK562CtcfInteractionsRep1 Interactions CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin Interaction Paired-End Tags Yijun Ruan Ruan - Genome Institute of Singapore (Chia) ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data. K562 CTCF ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan Regulation 
wgEncodeGisRnaSeq GIS RNA-seq GSE27221 RNA-seq from ENCODE/Genome Institute of Singapore Expression Description This track is produced as part of the ENCODE Transcriptome Project. It shows high throughput sequencing of RNA samples from tissues or sub cellular compartments from cell lines included in the ENCODE Transcriptome subproject. The overall goal of the ENCODE project is to identify and characterize all functional elements in the sequence of the human genome. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Color differences among the views are arbitrary. They provide a visual cue for distinguishing between the different cell types. Plus Raw Signal The Plus Raw Signal view graphs the base-by-base density of alignments on the + strand. Minus Raw Signal The Minus Raw Signal view graphs the base-by-base density of alignments on the - strand. Alignments The Alignments view shows reads mapped to the genome, both split alignments and alignments mapped to one exon. Sequences determined to be transcribed on the positive strand are shown in blue. Sequences determined to be transcribed on the negative strand are shown in red. Sequences for which the direction of transcription was not able to be determined are shown in black. For more information on the XL XJ and XU custom tags used in these files, please contact the producing lab. Please see the Bowtie Manual for more information about the SAM Bowtie output (including other tags) and the SAM Format Specification for more information on the SAM/BAM file format. Methods The RNA-Seq data were generated from high quality polyA RNA, and the RNA-Seq libraries were constructed using SOLiD Whole Transcriptome (WT) protocol and reagent kit. Total RNA in good quality was used as starting materials and purified twice through MACs polyT column aimed to enrich polyA and remove any contaminants (e.g., rRNA, tRNA, DNA, protein etc.). A one microgram enriched polyA RNA sample was then fragmented to small pieces, and a gel-based selection method was performed to collect fragmented random polyA at a size-range of 50-150 nt in length. The collected fragmental RNA was then hybridized and ligated to a mix of adapters provided from ABI, followed by reverse transcription to generate corresponding cDNAs. The resulting cDNA library was further amplified by PCR and sequenced by SOLiD platform for single reads at 35 bp length (new version in 50 bp length). Cells were grown according to the approved ENCODE cell culture protocols. Data: The SOLiD-generated RNA-Seq reads were 35 bp in length. An initial filtering process was performed to remove any non-desirable contamination sequences, such as rRNA, tRNA, and repeats etc. A read-split mapping approach was developed to map the 35 bp reads onto the reference genome (GRCh37/hg19) excluding mitochondrion, haplotypes, randoms and chromosome Y. Mapping parameters: Strand specific mapping was done using Applied Biosystems' SOLiD alignment where all the reads were mapped to the genome, and to exon-exon junction database. Seed and extend strategy is adopted where initial seed length of 25 is mapped with maximum of 2 mismatches and then extended to read length, each color space match is awarded a score of +1 and each mismatch is awarded a penalty of -2. After extension each read is trimmed to its maximum score, shortest length. The color space sequences are then converted into base space and checked to ensure that each sequence has a maximum of 2 base pair mismatches. If any sequence has more than 2 mismatches, then that sequence is discarded. Credits The GIS RNA-seq libraries and sequence data for transcriptome analysis were produced at the Genome Institute of Singapore. The data were mapped and analyzed by scientists from the Genome Institute of Singapore. Contact: RUAN Xiaoan Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeGisRnaSeqViewPlusRawSignal Plus Raw Signal RNA-seq from ENCODE/Genome Institute of Singapore Expression 
wgEncodeGisRnaSeqK562CytosolPapPlusRawRep2 K562 cyto pA+ + 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-01 2009-10-29 2010-07-29 wgEncodeEH000271 271 GSM672835 Gingeras GIS crg-55 cytosol hg18 2 longPolyA wgEncodeGisRnaSeqK562CytosolPapPlusRawRep2 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ RNA-seq Plus raw signal rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqK562CytosolPapPlusRawRep1 K562 cyto pA+ + 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-01 2009-10-29 2010-07-29 wgEncodeEH000271 271 GSM672833 Gingeras GIS crg-48 cytosol hg18 1 longPolyA wgEncodeGisRnaSeqK562CytosolPapPlusRawRep1 PlusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand K562 cytosol polyA+ RNA-seq Plus raw signal rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqH1hescCellPapPlusRawRep1 H1ES cell pA+ + 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-07-03 2009-10-29 2010-07-29 wgEncodeEH000270 270 GSM672836 Gingeras GIS crg-16 cell hg18 1 longPolyA wgEncodeGisRnaSeqH1hescCellPapPlusRawRep1 PlusRawSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore Whole cell Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand H1-hESC whole cell polyA+ RNA-seq Plus raw signal rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqGm12878CytosolPapPlusRawRep1 GM12 cyto pA+ + 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-07-03 2009-10-29 2010-07-29 wgEncodeEH000269 269 GSM672834 Gingeras GIS crg-9 cytosol hg18 1 longPolyA wgEncodeGisRnaSeqGm12878CytosolPapPlusRawRep1 PlusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the plus strand GM12878 cytosol polyA+ RNA-seq Plus raw signal rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqViewMinusRawSignal Minus Raw Signal RNA-seq from ENCODE/Genome Institute of Singapore Expression 
wgEncodeGisRnaSeqK562CytosolPapMinusRawRep2 K562 cyto pA+ - 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-01 2009-10-29 2010-07-29 wgEncodeEH000271 271 GSM672835 Gingeras GIS crg-55 cytosol hg18 2 longPolyA wgEncodeGisRnaSeqK562CytosolPapMinusRawRep2 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ RNA-seq Minus raw signal rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqK562CytosolPapMinusRawRep1 K562 cyto pA+ - 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-01 2009-10-29 2010-07-29 wgEncodeEH000271 271 GSM672833 Gingeras GIS crg-48 cytosol hg18 1 longPolyA wgEncodeGisRnaSeqK562CytosolPapMinusRawRep1 MinusRawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand K562 cytosol polyA+ RNA-seq Minus raw signal rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqH1hescCellPapMinusRawRep1 H1ES cell pA+ - 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-07-03 2009-10-29 2010-07-29 wgEncodeEH000270 270 GSM672836 Gingeras GIS crg-16 cell hg18 1 longPolyA wgEncodeGisRnaSeqH1hescCellPapMinusRawRep1 MinusRawSignal embryonic stem cells Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore Whole cell Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand H1-hESC whole cell polyA+ RNA-seq Minus raw signal rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqGm12878CytosolPapMinusRawRep1 GM12 cyto pA+ - 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-07-03 2009-10-29 2010-07-29 wgEncodeEH000269 269 GSM672834 Gingeras GIS crg-9 cytosol hg18 1 longPolyA wgEncodeGisRnaSeqGm12878CytosolPapMinusRawRep1 MinusRawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Graphs the base-by-base density of tags on the minus strand GM12878 cytosol polyA+ RNA-seq Minus raw signal rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqViewAlignments Alignments RNA-seq from ENCODE/Genome Institute of Singapore Expression 
wgEncodeGisRnaSeqK562CytosolPapAlnRep2 K562 cyto pA+ 2 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-01 2009-10-29 2010-07-29 wgEncodeEH000271 271 GSM672835 Gingeras GIS crg-55 cytosol hg18 2 longPolyA wgEncodeGisRnaSeqK562CytosolPapAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA+ RNA-seq Alignments rep 2 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqK562CytosolPapAlnRep1 K562 cyto pA+ 1 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-01 2009-10-29 2010-07-29 wgEncodeEH000271 271 GSM672833 Gingeras GIS crg-48 cytosol hg18 1 longPolyA wgEncodeGisRnaSeqK562CytosolPapAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch K562 cytosol polyA+ RNA-seq Alignments rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqH1hescCellPapAlnRep1 H1ES cell pA+ 1 H1-hESC RnaSeq ENCODE Jan 2011 Freeze 2010-07-03 2009-10-29 2010-07-29 wgEncodeEH000270 270 GSM672836 Gingeras GIS crg-16 cell hg18 1 longPolyA wgEncodeGisRnaSeqH1hescCellPapAlnRep1 Alignments embryonic stem cells Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore Whole cell Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch H1-hESC polyA+ RNA-seq Alignments rep 1 from ENCODE/GIS Expression 
wgEncodeGisRnaSeqGm12878CytosolPapAlnRep1 GM12 cyto pA+ 1 GM12878 RnaSeq ENCODE Jan 2011 Freeze 2010-07-03 2009-10-29 2010-07-29 wgEncodeEH000269 269 GSM672834 Gingeras GIS crg-9 cytosol hg18 1 longPolyA wgEncodeGisRnaSeqGm12878CytosolPapAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Sequencing analysis of RNA expression Gingeras Ruan - Genome Institute of Singapore The fluid between the cells outer membrane and the nucleus Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 cytosol polyA+ RNA-seq Alignments rep 1 from ENCODE/GIS Expression 
wgEncodeHaibMethylRrbs HAIB Methyl RRBS GSE27584 DNA Methylation by Reduced Representation Bisulfite Seq from ENCODE/HudsonAlpha Regulation Description This track was produced as part of the ENCODE project. The track reports the percentage of DNA molecules that exhibit cytosine methylation at specific CpG dinucleotides. In general, DNA methylation within a gene's promoter is associated with gene silencing and DNA methylation within the exons and introns of a gene is associated with gene expression. Proper regulation of DNA methylation is essential during development and aberrant DNA methylation is a hallmark of cancer. DNA methylation status was assayed at more than 500,000 CpG dinucleotides in the genome using Reduced Representation Bisulfite Sequencing (RRBS). Genomic DNA was digested with the methyl-insensitive restriction enzyme MspI and then small genomic DNA fragments were purified by gel electrophoresis and used to construct an Illumina sequencing library. The library fragments were treated with sodium bisulfite and amplified by PCR to convert every unmethylated cytosine to a thymidine while leaving methylated cytosines intact. The sequenced fragments were aligned to a customized reference genome sequence. For each assayed CpG, the number of sequencing reads covering that CpG and the percentage of those reads that were methylated were reported. Display Conventions and Configuration Methylation status is represented with an 11-color gradient using the following convention: red = 100% of molecules sequenced are methylated yellow = 50% of molecules sequenced are methylated green = 0% of molecules sequenced are methylated The score in this track reports the number of sequencing reads obtained for each CpG, which is often called 'coverage'. The score is capped at 1000, so any CpGs that were covered by more than 1000 sequencing reads have a score of 1000. The BED files available for download contain two extra columns: one with the uncapped coverage (number of reads at that site) and one with the percentage of those reads that show methylation. High reproducibility was obtained, with correlation coefficients greater than 0.9 between biological replicates, when only considering CpGs represented by at least 10 sequencing reads (10X coverage, score=10). Therefore, the default view for this track is set to 10X coverage, or a score of 10. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods DNA methylation at CpG sites was assayed with a modified version of Reduced Representation Bisulfite Sequencing (Meissner et al., 2008). RRBS was performed on cell lines grown by many ENCODE production groups. The production group that grew the cells and isolated genomic DNA is indicated in the "obtainedBy" field of the metadata. When a cell type was provided by more than one lab, the data from only one lab are available for immediate display. However, the data for every cell type from every lab is available from the Downloads page. RRBS was also performed on genomic DNA from tissue samples provided by BioChain. The replicates for the BioChain tissues are technical replicates (rather than biological replicates) beginning at the bisulfite treatment step. RRBS was carried out by the Myers production group at the HudsonAlpha Institute for Biotechnology. Isolation of Genomic DNA Genomic DNA was isolated from biological replicates of each cell line using the QIAGEN DNeasy Blood &amp; Tissue Kit according to the instructions provided by the manufacturer. DNA concentrations for each genomic DNA preparation were determined using fluorescent DNA binding dye and a fluorometer (Invitrogen Quant-iT dsDNA High Sensitivity Kit and Qubit Fluorometer). Typically, 1 &micro;g of DNA is used to make an RRBS library; however, there has been success in making libraries with 200 ng genomic DNA from rare or precious samples. RRBS Library Construction and Sequencing RRBS library construction started with MspI digestion of genomic DNA, which cut at every CCGG regardless of methylation status. Klenow exo- DNA Polymerase was then used to fill in the recessed end of the genomic DNA and add an adenosine as a 3' overhang. Next, a methylated version of the Illumina paired-end adapters was ligated onto the DNA. Adapter-ligated genomic DNA fragments between 105 and 185 base pairs were selected using agarose gel electrophoresis and a Qiagen Qiaquick Gel Extraction Kit. The selected adapter-ligated fragments were treated with sodium bisulfite using the Zymo Research EZ DNA Methylation Gold Kit, which converts unmethylated cytosines to uracils and leaves methylated cytosines unchanged. Bisulfite treated DNA was amplified in a final PCR reaction which was optimized to uniformly amplify diverse fragment sizes and sequence contexts in the same reaction. During this final PCR reaction, uracils were copied as thymines resulting in a thymine in the PCR products wherever an unmethylated cytosine existed in the genomic DNA. The sample was then ready for sequencing on the Illumina sequencing platform. These libraries were sequenced with an Illumina Genome Analyzer IIx according to the manufacturer's recommendations. The full RRBS protocol can be found here. Data Analysis To analyze the sequence data, a reference genome was created that contained only the 36 base pairs adjacent to every MspI site and in which every C was changed to a T. A converted sequence read file was then created by changing each C in the original sequence reads to a T. The converted sequence reads were aligned to the converted reference genome and only reads that mapped uniquely to the reference genome were kept. Once the reads were aligned, the percent methylation was calculated for each CpG using the original sequence reads. The percent methylation and number of reads were reported for each CpG. Release Notes This is Release 3 (July 2012) of this track which adds the MCF-7 cell line with shRNA knockdowns obtained from the Crawford Lab at Duke University. Credits These data were produced by the Dr. Richard Myers Lab at the HudsonAlpha Institute for Biotechnology. Cells were grown by the Myers Lab and other ENCODE production groups. Contact: Dr. Florencia Pauli References Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008 Aug 7;454(7205):766-70. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeDnaMethylSuper ENC DNA Methyl ENCODE DNA Methylation Regulation Description DNA methylation is essential for normal development and is associated with silencing large regions of DNA through processes such as imprinting and X-chromosome inactivation. The majority of CpG dinucleotides are methylated in mammals. Unmethylated CpGs occur in segments called "CpG islands", which often lie upstream of genes in the regulatory regions and impact transcription. Display Conventions These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Illingworth RS, Bird AP. CpG islands--'a rough guide'. FEBS Lett. 2009 Jun 5;583(11):1713-20. Caiafa P, Zampieri M. DNA methylation and chromatin structure: the puzzling CpG islands. J Cell Biochem. 2005 Feb 1;94(2):257-65. Latham T, Gilbert N, Ramsahoye B. DNA methylation in mouse embryonic stem cells and development. Cell Tissue Res. 2008 Jan;331(1):31-55. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeHaibMethylRrbsBcuterusbn0765BiochainSitesRep2 Uterus_BC 2 BC_Uterus_BN0765 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001400 1400 GSM683911 Myers HudsonAlpha SL3414 BioChain 2 wgEncodeHaibMethylRrbsBcuterusbn0765BiochainSitesRep2 None Sites uterus, donor BN0765, age 44, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Uterus BC BN0765 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcuterusbn0765BiochainSitesRep1 Uterus_BC 1 BC_Uterus_BN0765 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001400 1400 GSM683803 Myers HudsonAlpha SL1671 BioChain 1 wgEncodeHaibMethylRrbsBcuterusbn0765BiochainSitesRep1 None Sites uterus, donor BN0765, age 44, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Uterus BC BN0765 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsUch1DukeSitesRep2 UCH-1 2 UCH-1 MethylRrbs ENCODE Mar 2012 Freeze 2011-08-31 2012-05-31 wgEncodeEH002063 2063 GSM980581 Myers HudsonAlpha SL1821 Duke 2 wgEncodeHaibMethylRrbsUch1DukeSitesRep2 None Sites chordoma cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites UCH-1 Methyl RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsUch1DukeSitesRep1 UCH-1 1 UCH-1 MethylRrbs ENCODE Mar 2012 Freeze 2011-08-31 2012-05-31 wgEncodeEH002063 2063 GSM980581 Myers HudsonAlpha SL1814 Duke 1 wgEncodeHaibMethylRrbsUch1DukeSitesRep1 None Sites chordoma cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites UCH-1 Methyl RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsU87HaibSitesRep2 U87 2 U87 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001414 1414 GSM683890 Myers HudsonAlpha SL3558 HudsonAlpha 2 F wgEncodeHaibMethylRrbsU87HaibSitesRep2 None Sites glioblastoma, astrocytoma, (PMID: 4332744) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Female Sites U87 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsU87HaibSitesRep1 U87 1 U87 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001414 1414 GSM683917 Myers HudsonAlpha SL3557 HudsonAlpha 1 F wgEncodeHaibMethylRrbsU87HaibSitesRep1 None Sites glioblastoma, astrocytoma, (PMID: 4332744) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Female Sites U87 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBctestisn30BiochainSitesRep2 Testis_BC 2 BC_Testis_N30 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001399 1399 GSM683850 Myers HudsonAlpha SL3416 BioChain 2 wgEncodeHaibMethylRrbsBctestisn30BiochainSitesRep2 None Sites testis, donor N30, age 41, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Testis BC N30 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBctestisn30BiochainSitesRep1 Testis_BC  1 BC_Testis_N30 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001399 1399 GSM683781 Myers HudsonAlpha SL1677 BioChain 1 wgEncodeHaibMethylRrbsBctestisn30BiochainSitesRep1 None Sites testis, donor N30, age 41, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Testis BC N30 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep2 T-47D Estra 2 T-47D MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001413 1413 GSM683842 Myers HudsonAlpha SL1435 HudsonAlpha 2 wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep2 Estradiol_10nM_24hr Sites epithelial cell line derived from a mammary ductal carcinoma. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 24 hr with 10 nM Estradiol (Myers) Sites T-47D Estradiol Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep2 T-47D DMSO 2 T-47D MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001412 1412 GSM683771 Myers HudsonAlpha SL1436 HudsonAlpha 2 wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep2 DMSO_0.02pct_24hr Sites epithelial cell line derived from a mammary ductal carcinoma. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 24 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Sites T-47D DMSO 0.02% 24 h Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep1 T-47D Estra 1 T-47D MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001413 1413 GSM683904 Myers HudsonAlpha SL3484 HudsonAlpha 1 wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep1 Estradiol_10nM_24hr Sites epithelial cell line derived from a mammary ductal carcinoma. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 24 hr with 10 nM Estradiol (Myers) Sites T-47D Estradiol Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep1 T-47D DMSO 1 T-47D MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001412 1412 GSM683937 Myers HudsonAlpha SL3485 HudsonAlpha 1 wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep1 DMSO_0.02pct_24hr Sites epithelial cell line derived from a mammary ductal carcinoma. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 24 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Sites T-47D DMSO 0.02% 24 h Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcstomach0111002BiochainSitesRep2 Stomach_BC 2 BC_Stomach_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001398 1398 GSM683877 Myers HudsonAlpha SL3431 BioChain 2 wgEncodeHaibMethylRrbsBcstomach0111002BiochainSitesRep2 None Sites stomach, donor 01-11002, age 83, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Stomach BC 01-11002 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcstomach0111002BiochainSitesRep1 Stomach_BC 1 BC_Stomach_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001398 1398 GSM683947 Myers HudsonAlpha SL1997 BioChain 1 wgEncodeHaibMethylRrbsBcstomach0111002BiochainSitesRep1 None Sites stomach, donor 01-11002, age 83, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Stomach BC 01-11002 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSknshraUwSitesRep2 SK-N-SH_RA 2 SK-N-SH_RA MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001370 1370 GSM683919 Myers HudsonAlpha SL1628 UW 2 wgEncodeHaibMethylRrbsSknshraUwSitesRep2 None Sites neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-SH BC RA Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSknshraUwSitesRep1 SK-N-SH_RA 1 SK-N-SH_RA MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001370 1370 GSM683800 Myers HudsonAlpha SL863 UW 1 wgEncodeHaibMethylRrbsSknshraUwSitesRep1 None Sites neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-SH BC RA Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSknmcHaibSitesRep2 SK-N-MC 2 SK-N-MC MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001411 1411 GSM683918 Myers HudsonAlpha SL3554 HudsonAlpha 2 wgEncodeHaibMethylRrbsSknmcHaibSitesRep2 None Sites neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-MC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSknmcHaibSitesRep1 SK-N-MC 1 SK-N-MC MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001411 1411 GSM683884 Myers HudsonAlpha SL3553 HudsonAlpha 1 wgEncodeHaibMethylRrbsSknmcHaibSitesRep1 None Sites neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-MC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSkmcUwSitesRep2 SKMC 2 SKMC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001354 1354 GSM683784 Myers HudsonAlpha SL1419 UW 2 wgEncodeHaibMethylRrbsSkmcUwSitesRep2 None Sites skeletal muscle cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SKMC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSkmcUwSitesRep1 SKMC 1 SKMC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001354 1354 GSM683894 Myers HudsonAlpha SL886 UW 1 wgEncodeHaibMethylRrbsSkmcUwSitesRep1 None Sites skeletal muscle cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SKMC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcskin0111002BiochainSitesRep2 Skin BC 2 BC_Skin_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001397 1397 GSM683892 Myers HudsonAlpha SL3436 BioChain 2 wgEncodeHaibMethylRrbsBcskin0111002BiochainSitesRep2 None Sites skin, donor 01-11002, age 83, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Skin BC 01-11002 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcskin0111002BiochainSitesRep1 Skin BC 1 BC_Skin_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001397 1397 GSM683865 Myers HudsonAlpha SL1727 BioChain 1 wgEncodeHaibMethylRrbsBcskin0111002BiochainSitesRep1 None Sites skin, donor 01-11002, age 83, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Skin BC 01-11002 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcskeletalmuscleh12817nBiochainSitesRep2 Skeletal_7N 2 BC_Skeletal_Muscle_H12817N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001396 1396 GSM683868 Myers HudsonAlpha SL3441 BioChain 2 wgEncodeHaibMethylRrbsBcskeletalmuscleh12817nBiochainSitesRep2 None Sites skeletal muscle, donor H12817N, age 71, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Skeletal Muscle BC H12817N Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcskeletalmuscleh12817nBiochainSitesRep1 Skeletal_7N 1 BC_Skeletal_Muscle_H12817N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001396 1396 GSM683931 Myers HudsonAlpha SL1758 BioChain 1 wgEncodeHaibMethylRrbsBcskeletalmuscleh12817nBiochainSitesRep1 None Sites skeletal muscle, donor H12817N, age 71, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Skeletal Muscle BC H12817N Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcskeletalmuscle0111002BiochainSitesRep2 Skeletal_02 2 BC_Skeletal_Muscle_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001395 1395 GSM683811 Myers HudsonAlpha SL3439 BioChain 2 wgEncodeHaibMethylRrbsBcskeletalmuscle0111002BiochainSitesRep2 None Sites skeletal muscle, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Skeletal Muscle BC 01-11002 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcskeletalmuscle0111002BiochainSitesRep1 Skeletal_02 1 BC_Skeletal_Muscle_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001395 1395 GSM683789 Myers HudsonAlpha SL1752 BioChain 1 wgEncodeHaibMethylRrbsBcskeletalmuscle0111002BiochainSitesRep1 None Sites skeletal muscle, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Skeletal Muscle BC 01-11002 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSaecUwSitesRep2 SAEC 2 SAEC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001369 1369 GSM683833 Myers HudsonAlpha SL1342 UW 2 wgEncodeHaibMethylRrbsSaecUwSitesRep2 None Sites small airway epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SAEC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSaecUwSitesRep1 SAEC 1 SAEC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001369 1369 GSM683916 Myers HudsonAlpha SL864 UW 1 wgEncodeHaibMethylRrbsSaecUwSitesRep1 None Sites small airway epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SAEC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsRptecSitesRep2 RPTEC 2 RPTEC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001375 1375 GSM683772 Myers HudsonAlpha SL1346 UW 2 wgEncodeHaibMethylRrbsRptecSitesRep2 None Sites renal proximal tubule epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites RPTEC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsRptecSitesRep1 RPTEC 1 RPTEC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001375 1375 GSM683802 Myers HudsonAlpha SL876 UW 1 wgEncodeHaibMethylRrbsRptecSitesRep1 None Sites renal proximal tubule epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites RPTEC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsProgfibSitesRep2 ProgFib 2 ProgFib MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001374 1374 GSM683783 Myers HudsonAlpha SL1802 Duke 2 wgEncodeHaibMethylRrbsProgfibSitesRep2 None Sites fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites ProgFib Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsProgfibSitesRep1 ProgFib 1 ProgFib MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001374 1374 GSM683875 Myers HudsonAlpha SL938 Duke 1 wgEncodeHaibMethylRrbsProgfibSitesRep1 None Sites fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites ProgFib Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPrecUwSitesRep2 PrEC 2 PrEC MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001410 1410 GSM683760 Myers HudsonAlpha SL869 UW 2 wgEncodeHaibMethylRrbsPrecUwSitesRep2 None Sites prostate epithelial cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PrEC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPrecUwSitesRep1 PrEC 1 PrEC MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001410 1410 GSM683838 Myers HudsonAlpha SL868 UW 1 wgEncodeHaibMethylRrbsPrecUwSitesRep1 None Sites prostate epithelial cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PrEC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcplacentauhn00189BiochainSitesRep2 Placenta_BC 2 BC_Placenta_UHN00189 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001394 1394 GSM683893 Myers HudsonAlpha SL3413 BioChain 2 wgEncodeHaibMethylRrbsBcplacentauhn00189BiochainSitesRep2 None Sites placenta, donor UHN00189, age 29 DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Placenta BC UHN00189 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcplacentauhn00189BiochainSitesRep1 Placenta_BC 1 BC_Placenta_UHN00189 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001394 1394 GSM683796 Myers HudsonAlpha SL1675 BioChain 1 wgEncodeHaibMethylRrbsBcplacentauhn00189BiochainSitesRep1 None Sites placenta, donor UHN00189, age 29 DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Placenta BC UHN00189 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPfsk1HaibSitesRep2 PFSK-1 2 PFSK-1 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001409 1409 GSM683909 Myers HudsonAlpha SL3548 HudsonAlpha 2 wgEncodeHaibMethylRrbsPfsk1HaibSitesRep2 None Sites neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PFSK-1 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPfsk1HaibSitesRep1 PFSK-1 1 PFSK-1 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001409 1409 GSM683810 Myers HudsonAlpha SL3547 HudsonAlpha 1 wgEncodeHaibMethylRrbsPfsk1HaibSitesRep1 None Sites neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PFSK-1 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcpericardiumh12529nBiochainSitesRep2 Pericardium_BC 2 BC_Pericardium_H12529N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001393 1393 GSM683820 Myers HudsonAlpha SL3266 BioChain 2 wgEncodeHaibMethylRrbsBcpericardiumh12529nBiochainSitesRep2 None Sites pericardium, donor H12529N, age 70, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Pericardium BC H12529N Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcpericardiumh12529nBiochainSitesRep1 Pericardium_BC 1 BC_Pericardium_H12529N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001393 1393 GSM683899 Myers HudsonAlpha SL1674 BioChain 1 wgEncodeHaibMethylRrbsBcpericardiumh12529nBiochainSitesRep1 None Sites pericardium, donor H12529N, age 70, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Pericardium BC H12529N Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPanisletsSitesRep2 PanIslets 2 PanIslets MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001373 1373 GSM683934 Myers HudsonAlpha SL1941 Duke 2 wgEncodeHaibMethylRrbsPanisletsSitesRep2 None Sites pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PanIslets Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPanisletsSitesRep1 PanIslets 1 PanIslets MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001373 1373 GSM683874 Myers HudsonAlpha SL1937 Duke 1 wgEncodeHaibMethylRrbsPanisletsSitesRep1 None Sites pancreatic islets from 2 donors, the sources of these primary cells are cadavers from National Disease Research Interchange (NDRI) and another sample isolated as in Bucher, P. et al., Assessment of a novel two-component enzyme preparation for human islet isolation and transplantation. Transplantation 79, 917 (2005) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PanIslets Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcpancreash12817nBiochainSitesRep2 Pancreas_BC 2 BC_Pancreas_H12817N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001392 1392 GSM683819 Myers HudsonAlpha SL3442 BioChain 2 wgEncodeHaibMethylRrbsBcpancreash12817nBiochainSitesRep2 None Sites pancreas, donor H12817N, age 71, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Pancreas BC H12817N Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcpancreash12817nBiochainSitesRep1 Pancreas_BC 1 BC_Pancreas_H12817N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001392 1392 GSM683848 Myers HudsonAlpha SL1726 BioChain 1 wgEncodeHaibMethylRrbsBcpancreash12817nBiochainSitesRep1 None Sites pancreas, donor H12817N, age 71, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Pancreas BC H12817N Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPanc1UwSitesRep2 PANC-1 UW 2 PANC-1 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001408 1408 GSM1048458 Myers HudsonAlpha SL4743 UW 2 wgEncodeHaibMethylRrbsPanc1UwSitesRep2 None Sites pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PANC-1 UW Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPanc1HaibSitesRep2 PANC-1 HA 2 PANC-1 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001408 1408 GSM683920 Myers HudsonAlpha SL3552 HudsonAlpha 2 wgEncodeHaibMethylRrbsPanc1HaibSitesRep2 None Sites pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PANC-1 HAIB Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPanc1UwSitesRep1 PANC-1 UW 1 PANC-1 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001408 1408 GSM1048458 Myers HudsonAlpha SL861 UW 1 wgEncodeHaibMethylRrbsPanc1UwSitesRep1 None Sites pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PANC-1 UW Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsPanc1HaibSitesRep1 PANC-1 HA 1 PANC-1 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001408 1408 GSM683866 Myers HudsonAlpha SL3551 HudsonAlpha 1 wgEncodeHaibMethylRrbsPanc1HaibSitesRep1 None Sites pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites PANC-1 HAIB Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsOvcar3UwSitesRep2 Ovcar-3 2 ovcar-3 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001419 1419 GSM980577 Myers HudsonAlpha SL4746 UW 2 wgEncodeHaibMethylRrbsOvcar3UwSitesRep2 None Sites ovarian adenocarcinoma, "the NIH: OVCAR-3 line was established in 1982 by T.C. Hamilton, et al. from the malignant ascites of a patient with progressive adenocarcinoma of the ovary." - ATCC. (PMID: 6604576) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Ovcar-3 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsOvcar3UwSitesRep1 Ovcar-3 1 ovcar-3 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001419 1419 GSM980577 Myers HudsonAlpha SL904 UW 1 wgEncodeHaibMethylRrbsOvcar3UwSitesRep1 None Sites ovarian adenocarcinoma, "the NIH: OVCAR-3 line was established in 1982 by T.C. Hamilton, et al. from the malignant ascites of a patient with progressive adenocarcinoma of the ovary." - ATCC. (PMID: 6604576) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Ovcar-3 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsOsteoblDukeSitesRep2 Osteobl 2 Osteobl MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001381 1381 GSM683928 Myers HudsonAlpha SL1806 Duke 2 wgEncodeHaibMethylRrbsOsteoblDukeSitesRep2 None Sites osteoblasts (NHOst) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Osteoblasts Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsOsteoblDukeSitesRep1 Osteobl 1 Osteobl MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001381 1381 GSM683881 Myers HudsonAlpha SL767 Duke 1 wgEncodeHaibMethylRrbsOsteoblDukeSitesRep1 None Sites osteoblasts (NHOst) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Osteoblasts Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep2 NT2-D1 2 NT2-D1 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001353 1353 GSM683929 Myers HudsonAlpha SL1899 Stanford 2 wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep2 None Sites malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NT2-D1 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep1 NT2-D1 1 NT2-D1 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001353 1353 GSM720349 Myers HudsonAlpha SL758 Stanford 1 wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep1 None Sites malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NT2-D1 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNhdfneoUwSitesRep2 NHDF-neo 2 NHDF-neo MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001368 1368 GSM683861 Myers HudsonAlpha SL1376 UW 2 wgEncodeHaibMethylRrbsNhdfneoUwSitesRep2 None Sites neonatal dermal fibroblasts DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NHDF-neo Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNhdfneoUwSitesRep1 NHDF-neo 1 NHDF-neo MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001368 1368 GSM683797 Myers HudsonAlpha SL895 UW 1 wgEncodeHaibMethylRrbsNhdfneoUwSitesRep1 None Sites neonatal dermal fibroblasts DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NHDF-neo Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNhbeUwSitesRep2 NHBE 2 NHBE MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001352 1352 GSM683785 Myers HudsonAlpha SL1420 UW 2 wgEncodeHaibMethylRrbsNhbeUwSitesRep2 None Sites bronchial epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NHBE Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNhbeUwSitesRep1 NHBE 1 NHBE MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001352 1352 GSM683859 Myers HudsonAlpha SL871 UW 1 wgEncodeHaibMethylRrbsNhbeUwSitesRep1 None Sites bronchial epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NHBE Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNhaUwSitesRep2 NH-A 2 NH-A MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001380 1380 GSM683923 Myers HudsonAlpha SL1621 UW 2 wgEncodeHaibMethylRrbsNhaUwSitesRep2 None Sites astrocytes (also called Astrocy) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NH-A Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNhaUwSitesRep1 NH-A 1 NH-A MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001380 1380 GSM683873 Myers HudsonAlpha SL887 UW 1 wgEncodeHaibMethylRrbsNhaUwSitesRep1 None Sites astrocytes (also called Astrocy) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NH-A Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNb4UwSitesRep2 NB4 2 NB4 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001351 1351 GSM683827 Myers HudsonAlpha SL1442 UW 2 wgEncodeHaibMethylRrbsNb4UwSitesRep2 None Sites acute promyelocytic leukemia cell line. (PMID: 1995093) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NB4 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsNb4UwSitesRep1 NB4 1 NB4 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001351 1351 GSM683857 Myers HudsonAlpha SL872 UW 1 wgEncodeHaibMethylRrbsNb4UwSitesRep1 None Sites acute promyelocytic leukemia cell line. (PMID: 1995093) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites NB4 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMyometrDukeSitesRep2 Myometr 2 Myometr MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001407 1407 GSM683762 Myers HudsonAlpha SL3476 Duke 2 wgEncodeHaibMethylRrbsMyometrDukeSitesRep2 None Sites myometrial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Myometr Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMyometrDukeSitesRep1 Myometr 1 Myometr MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001407 1407 GSM683889 Myers HudsonAlpha SL3475 Duke 1 wgEncodeHaibMethylRrbsMyometrDukeSitesRep1 None Sites myometrial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Myometr Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMelanoSitesRep2 Melano 2 Melano MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001372 1372 GSM683840 Myers HudsonAlpha SL1809 Duke 2 wgEncodeHaibMethylRrbsMelanoSitesRep2 None Sites epidermal melanocytes DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Melano Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMelanoSitesRep1 Melano 1 Melano MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001372 1372 GSM683860 Myers HudsonAlpha SL1820 Duke 1 wgEncodeHaibMethylRrbsMelanoSitesRep1 None Sites epidermal melanocytes DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Melano Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2 MCF-7 CTCF 2 MCF-7 MethylRrbs ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEH003032 3032 GSM980574 Myers HudsonAlpha SL14362 Duke 2 wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2 CTCF_shRNA_knockdown Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. Sites MCF-7 shRNA CTCF knockdown Methyl RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2 MCF-7 Cont 2 MCF-7 MethylRrbs ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEH003033 3033 GSM980575 Myers HudsonAlpha SL14364 Duke 2 wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2 Randomized_shRNA_control Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. Sites MCF-7 shRNA Control Methyl RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1 MCF-7 CTCF 1 MCF-7 MethylRrbs ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEH003032 3032 GSM980574 Myers HudsonAlpha SL14361 Duke 1 wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1 CTCF_shRNA_knockdown Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct. Sites MCF-7 shRNA CTCF knockdown Methyl RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1 MCF-7 Cont 1 MCF-7 MethylRrbs ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEH003033 3033 GSM980575 Myers HudsonAlpha SL14363 Duke 1 wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1 Randomized_shRNA_control Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. Sites MCF-7 shRNA Control Methyl RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep2 MCF10A 2 MCF10A-Er-Src MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001378 1378 GSM683822 Myers HudsonAlpha SL730 Stanford 2 wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep2 None Sites mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites MCF10A Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep2 MCF10A Tam 2 MCF10A-Er-Src MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001379 1379 GSM683791 Myers HudsonAlpha SL733 Stanford 2 wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep2 4OHTAM_1uM_36hr Sites mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Sites MCF10A Tamoxifen Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep1 MCF10A 1 MCF10A-Er-Src MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001378 1378 GSM683896 Myers HudsonAlpha SL729 Stanford 1 wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep1 None Sites mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites MCF10A Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep1 MCF10A Tam 1 MCF10A-Er-Src MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001379 1379 GSM683853 Myers HudsonAlpha SL732 Stanford 1 wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep1 4OHTAM_1uM_36hr Sites mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Sites MCF10A Tamoxifen Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBclung0111002BiochainSitesRep2 Lung BC 2 BC_Lung_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001391 1391 GSM683940 Myers HudsonAlpha SL3433 BioChain 2 wgEncodeHaibMethylRrbsBclung0111002BiochainSitesRep2 None Sites lung, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Lung BC 01-11002 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBclung0111002BiochainSitesRep1 Lung BC 1 BC_Lung_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001391 1391 GSM683821 Myers HudsonAlpha SL1725 BioChain 1 wgEncodeHaibMethylRrbsBclung0111002BiochainSitesRep1 None Sites lung, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Lung BC 01-11002 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsLncapUwSitesRep2 LNCaP UW 2 LNCaP MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001406 1406 GSM683768 Myers HudsonAlpha SL3561 UW 2 wgEncodeHaibMethylRrbsLncapUwSitesRep2 None Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites LNCaP UW Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsLncapDukeSitesRep2 LNCaP Duke 2 LNCaP MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001406 1406 GSM683924 Myers HudsonAlpha SL3545 Duke 2 wgEncodeHaibMethylRrbsLncapDukeSitesRep2 None Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites LNCaP Duke Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep2 LNCaP Andro 2 LNCaP MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001367 1367 GSM683776 Myers HudsonAlpha SL1805 Duke 2 wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep2 androgen Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Sites LNCaP Androgen Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsLncapUwSitesRep1 LNCaP UW 1 LNCaP MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001406 1406 GSM683863 Myers HudsonAlpha SL907 UW 1 wgEncodeHaibMethylRrbsLncapUwSitesRep1 None Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites LNCaP UW Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsLncapDukeSitesRep1 LNCaP Duke 1 LNCaP MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001406 1406 GSM683862 Myers HudsonAlpha SL787 Duke 1 wgEncodeHaibMethylRrbsLncapDukeSitesRep1 None Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites LNCaP Duke Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep1 LNCaP Andro 1 LNCaP MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001367 1367 GSM683946 Myers HudsonAlpha SL1903 Duke 1 wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep1 androgen Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Sites LNCaP Androgen Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcliver0111002BiochainSitesRep2 Liver_BC 2 BC_Liver_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001390 1390 GSM683782 Myers HudsonAlpha SL3438 BioChain 2 wgEncodeHaibMethylRrbsBcliver0111002BiochainSitesRep2 None Sites liver, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Liver BC 01-11002 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcliver0111002BiochainSitesRep1 Liver BC 1 BC_Liver_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001390 1390 GSM683914 Myers HudsonAlpha SL1996 BioChain 1 wgEncodeHaibMethylRrbsBcliver0111002BiochainSitesRep1 None Sites liver, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Liver BC 01-11002 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcleukocyteuhn00204BiochainSitesRep2 Leukocyte_BC 2 BC_Leukocyte_UHN00204 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001389 1389 GSM683759 Myers HudsonAlpha SL3261 BioChain 2 wgEncodeHaibMethylRrbsBcleukocyteuhn00204BiochainSitesRep2 None Sites peripheral blood mononuclear cell, donor UHN00204, age 54, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Leukocyte BC UHN00204 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcleukocyteuhn00204BiochainSitesRep1 Leukocyte_BC 1 BC_Leukocyte_UHN00204 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001389 1389 GSM683876 Myers HudsonAlpha SL1755 BioChain 1 wgEncodeHaibMethylRrbsBcleukocyteuhn00204BiochainSitesRep1 None Sites peripheral blood mononuclear cell, donor UHN00204, age 54, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Leukocyte BC UHN00204 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep2 Ventricle_BC 2 BC_Left_Ventricle_N41 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001388 1388 GSM683895 Myers HudsonAlpha SL3264 BioChain 2 wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep2 None Sites left ventricle, donor N41, age 26, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Left Ventricle BC N41 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep1 Ventricle 1 BC_Left_Ventricle_N41 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001388 1388 GSM683846 Myers HudsonAlpha SL1722 BioChain 1 wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep1 None Sites left ventricle, donor N41, age 26, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Left Ventricle BC N41 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBckidney0111002BiochainSitesRep2 Kidney_BC 2 BC_Kidney_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001387 1387 GSM683878 Myers HudsonAlpha SL3435 BioChain 2 wgEncodeHaibMethylRrbsBckidney0111002BiochainSitesRep2 None Sites kidney, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Kidney BC 01-11002 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBckidney0111002BiochainSitesRep1 Kidney_BC 1 BC_Kidney_01-11002 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001387 1387 GSM683870 Myers HudsonAlpha SL1751 BioChain 1 wgEncodeHaibMethylRrbsBckidney0111002BiochainSitesRep1 None Sites kidney, donor 01-11002, age 83, caucasian, DNA and RNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Kidney BC 01-11002 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsJurkatUwSitesRep2 Jurkat 2 Jurkat MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001359 1359 GSM683806 Myers HudsonAlpha SL1345 UW 2 wgEncodeHaibMethylRrbsJurkatUwSitesRep2 None Sites T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Jurkati Methyl-RRBS Rep 2  from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsJurkatUwSitesRep1 Jurkat 1 Jurkat MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001359 1359 GSM683792 Myers HudsonAlpha SL899 UW 1 wgEncodeHaibMethylRrbsJurkatUwSitesRep1 None Sites T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Jurkat Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHtr8DukeSitesRep3 HTR8svn 2 HTR8svn MethylRrbs ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH001415 1415 GSM683867 Myers HudsonAlpha SL1811 Duke 3 wgEncodeHaibMethylRrbsHtr8DukeSitesRep3 None Sites trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HTR-8svn Methyl-RRBS Rep 2 (Lab Rep 3) from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHtr8DukeSitesRep1 HTR8svn 1 HTR8svn MethylRrbs ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH001415 1415 GSM683939 Myers HudsonAlpha SL3474 Duke 1 wgEncodeHaibMethylRrbsHtr8DukeSitesRep1 None Sites trophoblast (HTR-8/SVneo) cell line, a thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HTR-8svn Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep3 HSMMtube_FSHD 3 HSMMtube_FSHD MethylRrbs ENCODE Mar 2012 Freeze 2011-08-26 2012-05-26 wgEncodeEH002061 2061 GSM980579 Myers HudsonAlpha SL1918 Duke 3 wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep3 None Sites myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMMtube FSHD Methyl RRBS Rep 3 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep2 HSMMtube_FSHD 2 HSMMtube_FSHD MethylRrbs ENCODE Mar 2012 Freeze 2011-08-26 2012-05-26 wgEncodeEH002061 2061 GSM980579 Myers HudsonAlpha SL1921 Duke 2 wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep2 None Sites myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMMtube FSHD Methyl RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep1 HSMMtube_FSHD 1 HSMMtube_FSHD MethylRrbs ENCODE Mar 2012 Freeze 2011-08-26 2012-05-26 wgEncodeEH002061 2061 GSM980579 Myers HudsonAlpha SL1920 Duke 1 wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep1 None Sites myotube from Facioscapulohumeral Muscular Dystrophy (FSHD) patient, muscle needle biopsies DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMMtube FSHD Methyl RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmtDukeSitesRep3 HSMMtube 3 HSMMtube MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001348 1348 GSM683801 Myers HudsonAlpha SL1915 Duke 3 wgEncodeHaibMethylRrbsHsmmtDukeSitesRep3 None Sites skeletal muscle myotubes differentiated from the HSMM cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMMtube Methyl-RRBS Rep 3 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmtDukeSitesRep2 HSMMtube 2 HSMMtube MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001348 1348 GSM683799 Myers HudsonAlpha SL1935 Duke 2 wgEncodeHaibMethylRrbsHsmmtDukeSitesRep2 None Sites skeletal muscle myotubes differentiated from the HSMM cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMMtube Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmtDukeSitesRep1 HSMMtube 1 HSMMtube MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001348 1348 GSM683945 Myers HudsonAlpha SL1916 Duke 1 wgEncodeHaibMethylRrbsHsmmtDukeSitesRep1 None Sites skeletal muscle myotubes differentiated from the HSMM cell line DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMMtube Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep3 HSMM_FSHD 3 HSMM_FSHD MethylRrbs ENCODE Mar 2012 Freeze 2011-08-26 2012-05-26 wgEncodeEH002060 2060 GSM980578 Myers HudsonAlpha SL1917 Duke 3 wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep3 None Sites primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMM FSHD Methyl RRBS Rep 3 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep2 HSMM_FSHD 2 HSMM_FSHD MethylRrbs ENCODE Mar 2012 Freeze 2011-08-26 2012-05-26 wgEncodeEH002060 2060 GSM980578 Myers HudsonAlpha SL1936 Duke 2 wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep2 None Sites primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMM FSHD Methyl RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep1 HSMM_FSHD 1 HSMM_FSHD MethylRrbs ENCODE Mar 2012 Freeze 2011-08-26 2012-05-26 wgEncodeEH002060 2060 GSM980578 Myers HudsonAlpha SL1919 Duke 1 wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep1 None Sites primary myoblast from Facioscapulohumeral Muscular Dystrophy (FSHD) patients, muscle needle biopsies DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMM FSHD Methyl RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmDukeSitesRep2 HSMM 2 HSMM MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001371 1371 GSM683907 Myers HudsonAlpha SL940 Duke 2 wgEncodeHaibMethylRrbsHsmmDukeSitesRep2 None Sites skeletal muscle myoblasts DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMM Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHsmmDukeSitesRep1 HSMM 1 HSMM MethylRrbs ENCODE Jan 2011 Freeze 2010-09-29 2011-06-29 wgEncodeEH001371 1371 GSM683818 Myers HudsonAlpha SL939 Duke 1 wgEncodeHaibMethylRrbsHsmmDukeSitesRep1 None Sites skeletal muscle myoblasts DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HSMM Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHrpeUwSitesRep2 HRPEpiC 2 HRPEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001358 1358 GSM683905 Myers HudsonAlpha SL1443 UW 2 wgEncodeHaibMethylRrbsHrpeUwSitesRep2 None Sites retinal pigment epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRPEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHrpeUwSitesRep1 HRPEpiC 1 HRPEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001358 1358 GSM683773 Myers HudsonAlpha SL874 UW 1 wgEncodeHaibMethylRrbsHrpeUwSitesRep1 None Sites retinal pigment epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRPEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHreUwSitesRep2 HRE 2 HRE MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001357 1357 GSM683943 Myers HudsonAlpha SL1343 UW 2 wgEncodeHaibMethylRrbsHreUwSitesRep2 None Sites renal epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRE Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHreUwSitesRep1 HRE 1 HRE MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001357 1357 GSM683831 Myers HudsonAlpha SL865 UW 1 wgEncodeHaibMethylRrbsHreUwSitesRep1 None Sites renal epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRE Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHrceUwSitesRep2 HRCEpiC 2 HRCEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001347 1347 GSM683851 Myers HudsonAlpha SL1344 UW 2 wgEncodeHaibMethylRrbsHrceUwSitesRep2 None Sites renal cortical epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRCEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHrceUwSitesRep1 HRCEpiC 1 HRCEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001347 1347 GSM683901 Myers HudsonAlpha SL866 UW 1 wgEncodeHaibMethylRrbsHrceUwSitesRep1 None Sites renal cortical epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRCEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHpaeUwSitesRep2 HPAEpiC 2 HPAEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001366 1366 GSM683913 Myers HudsonAlpha SL1347 UW 2 wgEncodeHaibMethylRrbsHpaeUwSitesRep2 None Sites pulmonary alveolar epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HPAEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHpaeUwSitesRep1 HPAEpiC 1 HPAEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001366 1366 GSM683794 Myers HudsonAlpha SL897 UW 1 wgEncodeHaibMethylRrbsHpaeUwSitesRep1 None Sites pulmonary alveolar epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HPAEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHnpceUwSitesRep2 HNPCEpiC 2 HNPCEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001346 1346 GSM683808 Myers HudsonAlpha SL1440 UW 2 wgEncodeHaibMethylRrbsHnpceUwSitesRep2 None Sites non-pigment ciliary epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HNPCEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHnpceUwSitesRep1 HNPCEpiC 1 HNPCEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001346 1346 GSM683844 Myers HudsonAlpha SL877 UW 1 wgEncodeHaibMethylRrbsHnpceUwSitesRep1 None Sites non-pigment ciliary epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HNPCEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHmecUwSitesRep2 HMEC 2 HMEC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001345 1345 GSM683854 Myers HudsonAlpha SL1421 UW 2 wgEncodeHaibMethylRrbsHmecUwSitesRep2 None Sites mammary epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HMEC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHmecUwSitesRep1 HMEC 1 HMEC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001345 1345 GSM683944 Myers HudsonAlpha SL867 UW 1 wgEncodeHaibMethylRrbsHmecUwSitesRep1 None Sites mammary epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HMEC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHl60UwSitesRep2 HL-60 2 HL-60 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001418 1418 GSM980576 Myers HudsonAlpha SL4742 UW 2 wgEncodeHaibMethylRrbsHl60UwSitesRep2 None Sites promyelocytic leukemia cells, (PMID: 276884) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HL-60 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHl60UwSitesRep1 HL-60 1 HL-60 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001418 1418 GSM980576 Myers HudsonAlpha SL902 UW 1 wgEncodeHaibMethylRrbsHl60UwSitesRep1 None Sites promyelocytic leukemia cells, (PMID: 276884) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HL-60 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHipeUwSitesRep2 HIPEpiC 2 HIPEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001344 1344 GSM683942 Myers HudsonAlpha SL1619 UW 2 wgEncodeHaibMethylRrbsHipeUwSitesRep2 None Sites iris pigment epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HIPEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHipeUwSitesRep1 HIPEpiC 1 HIPEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001344 1344 GSM683816 Myers HudsonAlpha SL875 UW 1 wgEncodeHaibMethylRrbsHipeUwSitesRep1 None Sites iris pigment epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HIPEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHepatocytesDukeSitesRep2 Hepatocytes 2 Hepatocytes MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001405 1405 GSM683872 Myers HudsonAlpha SL1807 Duke 2 wgEncodeHaibMethylRrbsHepatocytesDukeSitesRep2 None Sites primary hepatocytes, liver perfused by enzymes to generate single cell suspension DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Hepatocytes Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHepatocytesDukeSitesRep1 Hepatocytes 1 Hepatocytes MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001405 1405 GSM683764 Myers HudsonAlpha SL1819 Duke 1 wgEncodeHaibMethylRrbsHepatocytesDukeSitesRep1 None Sites primary hepatocytes, liver perfused by enzymes to generate single cell suspension DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Hepatocytes Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHek293UwSitesRep2 HEK293 UW 2 HEK293 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001343 1343 GSM683769 Myers HudsonAlpha SL1422 UW 2 wgEncodeHaibMethylRrbsHek293UwSitesRep2 None Sites embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEK293 UW Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHek293StanfordSitesRep2 HEK293 St 2 HEK293 MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001343 1343 GSM720354 Myers HudsonAlpha SL1901 Stanford 2 wgEncodeHaibMethylRrbsHek293StanfordSitesRep2 None Sites embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEK293 St Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHek293UwSitesRep1 HEK293 UW 1 HEK293 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001343 1343 GSM683825 Myers HudsonAlpha SL860 UW 1 wgEncodeHaibMethylRrbsHek293UwSitesRep1 None Sites embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEK293 UW Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHek293StanfordSitesRep1 HEK293 St 1 HEK293 MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001343 1343 GSM720355 Myers HudsonAlpha SL759 Stanford 1 wgEncodeHaibMethylRrbsHek293StanfordSitesRep1 None Sites embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEK293 St Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHeeUwSitesRep2 HEEpiC 2 HEEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001342 1342 GSM683807 Myers HudsonAlpha SL1620 UW 2 wgEncodeHaibMethylRrbsHeeUwSitesRep2 None Sites esophageal epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHeeUwSitesRep1 HEEpiC 1 HEEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001342 1342 GSM683839 Myers HudsonAlpha SL896 UW 1 wgEncodeHaibMethylRrbsHeeUwSitesRep1 None Sites esophageal epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHct116StanfordSitesRep2 HCT-116 2 HCT-116 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001356 1356 GSM683898 Myers HudsonAlpha SL1902 Stanford 2 wgEncodeHaibMethylRrbsHct116StanfordSitesRep2 None Sites colorectal carcinoma (PMID: 7214343) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCT-116 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHct116StanfordSitesRep1 HCT-116 1 HCT-116 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001356 1356 GSM683788 Myers HudsonAlpha SL757 Stanford 1 wgEncodeHaibMethylRrbsHct116StanfordSitesRep1 None Sites colorectal carcinoma (PMID: 7214343) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCT-116 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHcpeUwSitesRep2 HCPEpiC 2 HCPEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001365 1365 GSM683849 Myers HudsonAlpha SL1439 UW 2 wgEncodeHaibMethylRrbsHcpeUwSitesRep2 None Sites choroid plexus epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCPEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHcpeUwSitesRep1 HCPEpiC 1 HCPEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-09-22 2011-06-22 wgEncodeEH001365 1365 GSM683936 Myers HudsonAlpha SL892 UW 1 wgEncodeHaibMethylRrbsHcpeUwSitesRep1 None Sites choroid plexus epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCPEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHcmUwSitesRep2 HCM 2 HCM MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001341 1341 GSM683922 Myers HudsonAlpha SL1626 UW 2 wgEncodeHaibMethylRrbsHcmUwSitesRep2 None Sites cardiac myocytes DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCM Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHcmUwSitesRep1 HCM 1 HCM MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001341 1341 GSM683852 Myers HudsonAlpha SL873 UW 1 wgEncodeHaibMethylRrbsHcmUwSitesRep1 None Sites cardiac myocytes DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCM Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHcfUwSitesRep2 HCF 2 HCF MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001340 1340 GSM683829 Myers HudsonAlpha SL1441 UW 2 wgEncodeHaibMethylRrbsHcfUwSitesRep2 None Sites cardiac fibroblasts DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCF Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHcfUwSitesRep1 HCF 1 HCF MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001340 1340 GSM683837 Myers HudsonAlpha SL898 UW 1 wgEncodeHaibMethylRrbsHcfUwSitesRep1 None Sites cardiac fibroblasts DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCF Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHaeUwSitesRep2 HAEpiC 2 HAEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001339 1339 GSM683858 Myers HudsonAlpha SL1618 UW 2 wgEncodeHaibMethylRrbsHaeUwSitesRep2 None Sites amniotic epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HAEpiC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHaeUwSitesRep1 HAEpiC 1 HAEpiC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001339 1339 GSM683824 Myers HudsonAlpha SL889 UW 1 wgEncodeHaibMethylRrbsHaeUwSitesRep1 None Sites amniotic epithelial cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HAEpiC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm19240DukeSitesRep2 GM19240 2 GM19240 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001338 1338 GSM683938 Myers HudsonAlpha SL1803 Duke 2 wgEncodeHaibMethylRrbsGm19240DukeSitesRep2 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM19240 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm19240DukeSitesRep1 GM19240 1 GM19240 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001338 1338 GSM683777 Myers HudsonAlpha SL943 Duke 1 wgEncodeHaibMethylRrbsGm19240DukeSitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM19240 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm19239DukeSitesRep2 GM19239 2 GM19239 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001337 1337 GSM683843 Myers HudsonAlpha SL793 Duke 2 wgEncodeHaibMethylRrbsGm19239DukeSitesRep2 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM19239 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm19239DukeSitesRep1 GM19239 1 GM19239 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001337 1337 GSM683903 Myers HudsonAlpha SL1804 Duke 1 wgEncodeHaibMethylRrbsGm19239DukeSitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM19239 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12892HaibSitesRep2 GM12892 2 GM12892 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001361 1361 GSM683887 Myers HudsonAlpha SL760 HudsonAlpha 2 wgEncodeHaibMethylRrbsGm12892HaibSitesRep2 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12892 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12892HaibSitesRep1 GM12892 1 GM12892 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001361 1361 GSM683902 Myers HudsonAlpha SL761 HudsonAlpha 1 wgEncodeHaibMethylRrbsGm12892HaibSitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12892 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12891HaibSitesRep2 GM12891 2 GM12891 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001360 1360 GSM683921 Myers HudsonAlpha SL1233 HudsonAlpha 2 wgEncodeHaibMethylRrbsGm12891HaibSitesRep2 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12891 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12891HaibSitesRep1 GM12891 1 GM12891 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001360 1360 GSM683835 Myers HudsonAlpha SL1232 HudsonAlpha 1 wgEncodeHaibMethylRrbsGm12891HaibSitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12891 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12878ximatHaibSitesRep2 GM12878-XiM 2 GM12878-XiMat MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001376 1376 GSM683841 Myers HudsonAlpha SL1614 HudsonAlpha 2 wgEncodeHaibMethylRrbsGm12878ximatHaibSitesRep2 None Sites B-lymphocyte, lymphoblastoid, cloned for maternal X inactivation, International HapMap Project, CEPH/Utah, Epstein-Barr Virus DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12878-XiMat Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12878ximatHaibSitesRep1 GM12878-XiM 1 GM12878-XiMat MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001376 1376 GSM683774 Myers HudsonAlpha SL1615 HudsonAlpha 1 wgEncodeHaibMethylRrbsGm12878ximatHaibSitesRep1 None Sites B-lymphocyte, lymphoblastoid, cloned for maternal X inactivation, International HapMap Project, CEPH/Utah, Epstein-Barr Virus DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12878-XiMat Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm06990UwSitesRep2 GM06990 2 GM06990 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001417 1417 GSM980583 Myers HudsonAlpha SL4745 UW 2 wgEncodeHaibMethylRrbsGm06990UwSitesRep2 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM06990 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm06990UwSitesRep1 GM06990 1 GM06990 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001417 1417 GSM980583 Myers HudsonAlpha SL901 UW 1 wgEncodeHaibMethylRrbsGm06990UwSitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM06990 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsFibroblDukeSitesRep2 Fibrobl 2 Fibrobl MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001336 1336 GSM683847 Myers HudsonAlpha SL1818 Duke 2 wgEncodeHaibMethylRrbsFibroblDukeSitesRep2 None Sites child fibroblast DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Fibrobl Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsFibroblDukeSitesRep1 Fibrobl 1 Fibrobl MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001336 1336 GSM683766 Myers HudsonAlpha SL765 Duke 1 wgEncodeHaibMethylRrbsFibroblDukeSitesRep1 None Sites child fibroblast DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Fibrobl Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsEcc1HaibSitesRep2 ECC-1 2 ECC-1 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001403 1403 GSM683925 Myers HudsonAlpha SL3483 HudsonAlpha 2 wgEncodeHaibMethylRrbsEcc1HaibSitesRep2 None Sites epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites ECC-1 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsEcc1HaibSitesRep1 ECC-1 1 ECC-1 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001403 1403 GSM683845 Myers HudsonAlpha SL3482 HudsonAlpha 1 wgEncodeHaibMethylRrbsEcc1HaibSitesRep1 None Sites epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites ECC-1 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsCmkUwSitesRep2 CMK 2 CMK MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001335 1335 GSM683930 Myers HudsonAlpha SL1341 UW 2 wgEncodeHaibMethylRrbsCmkUwSitesRep2 None Sites acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites CMK Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsCmkUwSitesRep1 CMK 1 CMK MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001335 1335 GSM683778 Myers HudsonAlpha SL870 UW 1 wgEncodeHaibMethylRrbsCmkUwSitesRep1 None Sites acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites CMK Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsCaco2UwSitesRep2 Caco-2 2 Caco-2 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001416 1416 GSM980582 Myers HudsonAlpha SL4744 UW 2 wgEncodeHaibMethylRrbsCaco2UwSitesRep2 None Sites colorectal adenocarcinoma. (PMID: 1939345) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Caco-2 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsCaco2UwSitesRep1 Caco-2 1 Caco-2 MethylRrbs ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001416 1416 GSM980582 Myers HudsonAlpha SL862 UW 1 wgEncodeHaibMethylRrbsCaco2UwSitesRep1 None Sites colorectal adenocarcinoma. (PMID: 1939345) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Caco-2 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcbreast0203015BiochainSitesRep2 Breast BC 2 BC_Breast_02-03015 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001386 1386 GSM683761 Myers HudsonAlpha SL3430 BioChain 2 wgEncodeHaibMethylRrbsBcbreast0203015BiochainSitesRep2 None Sites breast, donor 02-03015, age 21, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Breast BC 02-03015 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcbreast0203015BiochainSitesRep1 Breast_BC 1 BC_Breast_02-03015 MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001386 1386 GSM683834 Myers HudsonAlpha SL1673 BioChain 1 wgEncodeHaibMethylRrbsBcbreast0203015BiochainSitesRep1 None Sites breast, donor 02-03015, age 21, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Breast BC 02-03015 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcbrainh11058nBiochainSitesRep2 Brain_BC 2 BC_Brain_H11058N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001385 1385 GSM683798 Myers HudsonAlpha SL3267 BioChain 2 wgEncodeHaibMethylRrbsBcbrainh11058nBiochainSitesRep2 None Sites brain, donor H11058N, age 66, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Brain BC H11058N Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcbrainh11058nBiochainSitesRep1 Brain_BC 1 BC_Brain_H11058N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001385 1385 GSM683908 Myers HudsonAlpha SL1672 BioChain 1 wgEncodeHaibMethylRrbsBcbrainh11058nBiochainSitesRep1 None Sites brain, donor H11058N, age 66, Asian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Brain BC H11058N Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBjUwSitesRep2 BJ 2 BJ MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001402 1402 GSM683763 Myers HudsonAlpha SL3560 UW 2 wgEncodeHaibMethylRrbsBjUwSitesRep2 None Sites skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites BJ Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBjUwSitesRep1 BJ 1 BJ MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001402 1402 GSM683779 Myers HudsonAlpha SL903 UW 1 wgEncodeHaibMethylRrbsBjUwSitesRep1 None Sites skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites BJ Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBe2cHaibSitesRep2 BE2_C 2 BE2_C MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001401 1401 GSM683869 Myers HudsonAlpha SL3556 HudsonAlpha 2 wgEncodeHaibMethylRrbsBe2cHaibSitesRep2 None Sites neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites BE2 C Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBe2cHaibSitesRep1 BE2_C 1 BE2_C MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001401 1401 GSM683885 Myers HudsonAlpha SL3555 HudsonAlpha 1 wgEncodeHaibMethylRrbsBe2cHaibSitesRep1 None Sites neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites BE2 C Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAosmcDukeSitesRep2 AoSMC 2 AoSMC MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001382 1382 GSM683910 Myers HudsonAlpha SL3546 Duke 2 wgEncodeHaibMethylRrbsAosmcDukeSitesRep2 None Sites aortic smooth muscle cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AoSMC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAosmcDukeSitesRep1 AoSMC 1 AoSMC MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001382 1382 GSM683814 Myers HudsonAlpha SL766 Duke 1 wgEncodeHaibMethylRrbsAosmcDukeSitesRep1 None Sites aortic smooth muscle cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AoSMC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg10803UwSitesRep2 AG10803 2 AG10803 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001334 1334 GSM683912 Myers HudsonAlpha SL1438 UW 2 wgEncodeHaibMethylRrbsAg10803UwSitesRep2 None Sites abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG10803 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg10803UwSitesRep1 AG10803 1 AG10803 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001334 1334 GSM683809 Myers HudsonAlpha SL891 UW 1 wgEncodeHaibMethylRrbsAg10803UwSitesRep1 None Sites abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG10803 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg09319UwSitesRep2 AG09319 2 AG09319 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001333 1333 GSM683864 Myers HudsonAlpha SL1418 UW 2 wgEncodeHaibMethylRrbsAg09319UwSitesRep2 None Sites gum tissue fibroblasts from apparently heathly 24 year old DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG09319 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg09319UwSitesRep1 AG09319 1 AG09319 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001333 1333 GSM683915 Myers HudsonAlpha SL894 UW 1 wgEncodeHaibMethylRrbsAg09319UwSitesRep1 None Sites gum tissue fibroblasts from apparently heathly 24 year old DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG09319 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg09309UwSitesRep2 AG09309 2 AG09309 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001332 1332 GSM683886 Myers HudsonAlpha SL1437 UW 2 wgEncodeHaibMethylRrbsAg09309UwSitesRep2 None Sites adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG09309 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg09309UwSitesRep1 AG09309 1 AG09309 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001332 1332 GSM683767 Myers HudsonAlpha SL888 UW 1 wgEncodeHaibMethylRrbsAg09309UwSitesRep1 None Sites adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG09309 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg04450UwSitesRep2 AG04450 2 AG04450 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001331 1331 GSM683880 Myers HudsonAlpha SL1417 UW 2 wgEncodeHaibMethylRrbsAg04450UwSitesRep2 None Sites fetal lung fibroblast DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG04450 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg04450UwSitesRep1 AG04450 1 AG04450 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001331 1331 GSM683817 Myers HudsonAlpha SL893 UW 1 wgEncodeHaibMethylRrbsAg04450UwSitesRep1 None Sites fetal lung fibroblast DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG04450 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg04449UwSitesRep2 AG04449 2 AG04449 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001330 1330 GSM683897 Myers HudsonAlpha SL1625 UW 2 wgEncodeHaibMethylRrbsAg04449UwSitesRep2 None Sites fetal buttock/thigh fibroblast DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG04449 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsAg04449UwSitesRep1 AG04449 1 AG04449 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001330 1330 GSM683830 Myers HudsonAlpha SL890 UW 1 wgEncodeHaibMethylRrbsAg04449UwSitesRep1 None Sites fetal buttock/thigh fibroblast DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG04449 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcadrenalglandh12803nBiochainSitesRep2 Adrenal_BC 2 BC_Adrenal_Gland_H12803N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001384 1384 GSM683883 Myers HudsonAlpha SL3265 BioChain 2 wgEncodeHaibMethylRrbsBcadrenalglandh12803nBiochainSitesRep2 None Sites adrenal gland, donor H12803N, age 88, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Adrenal Gland BC H12803N Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsBcadrenalglandh12803nBiochainSitesRep1 Adrenal_BC 1 BC_Adrenal_Gland_H12803N MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001384 1384 GSM683786 Myers HudsonAlpha SL1676 BioChain 1 wgEncodeHaibMethylRrbsBcadrenalglandh12803nBiochainSitesRep1 None Sites adrenal gland, donor H12803N, age 88, caucasian, DNA extract DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites Adrenal Gland BC H12803N Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSknshHaibSitesRep2 SK-N-SH 2 SK-N-SH MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001404 1404 GSM683775 Myers HudsonAlpha SL3550 HudsonAlpha 2 wgEncodeHaibMethylRrbsSknshHaibSitesRep2 None Sites neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-SH Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsSknshHaibSitesRep1 SK-N-SH 1 SK-N-SH MethylRrbs ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001404 1404 GSM683888 Myers HudsonAlpha SL3549 HudsonAlpha 1 wgEncodeHaibMethylRrbsSknshHaibSitesRep1 None Sites neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-SH Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf7DukeSitesRep2 MCF-7 2 MCF-7 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001350 1350 GSM683793 Myers HudsonAlpha SL1813 Duke 2 wgEncodeHaibMethylRrbsMcf7DukeSitesRep2 None Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites MCF-7 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsMcf7DukeSitesRep1 MCF-7 1 MCF-7 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001350 1350 GSM683787 Myers HudsonAlpha SL1812 Duke 1 wgEncodeHaibMethylRrbsMcf7DukeSitesRep1 None Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites MCF-7 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsImr90UwSitesRep2 IMR90 2 IMR90 MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001377 1377 GSM683815 Myers HudsonAlpha SL1375 UW 2 wgEncodeHaibMethylRrbsImr90UwSitesRep2 None Sites fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites IMR90 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsImr90UwSitesRep1 IMR90 1 IMR90 MethylRrbs ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001377 1377 GSM683823 Myers HudsonAlpha SL900 UW 1 wgEncodeHaibMethylRrbsImr90UwSitesRep1 None Sites fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites IMR90 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHepg2DukeSitesRep2 HepG2 2 HepG2 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001349 1349 GSM683855 Myers HudsonAlpha SL1816 Duke 2 wgEncodeHaibMethylRrbsHepg2DukeSitesRep2 None Sites hepatocellular carcinoma DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HepG2 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHepg2DukeSitesRep1 HepG2 1 HepG2 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-13 2011-04-13 wgEncodeEH001349 1349 GSM683795 Myers HudsonAlpha SL1815 Duke 1 wgEncodeHaibMethylRrbsHepg2DukeSitesRep1 None Sites hepatocellular carcinoma DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HepG2 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHelas3HaibSitesRep2 HeLa-S3 2 HeLa-S3 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001363 1363 GSM683828 Myers HudsonAlpha SL712 HudsonAlpha 2 wgEncodeHaibMethylRrbsHelas3HaibSitesRep2 None Sites cervical carcinoma DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HeLa-S3 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsHelas3HaibSitesRep1 HeLa-S3 1 HeLa-S3 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001363 1363 GSM683926 Myers HudsonAlpha SL657 HudsonAlpha 1 wgEncodeHaibMethylRrbsHelas3HaibSitesRep1 None Sites cervical carcinoma DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites HeLa-S3 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsA549Dm002p7dHaibSitesRep2 A549 2 A549 MethylRrbs ENCODE Mar 2012 Freeze 2011-08-31 2012-05-31 wgEncodeEH002062 2062 GSM980580 Myers HudsonAlpha SL3656 HudsonAlpha 2 wgEncodeHaibMethylRrbsA549Dm002p7dHaibSitesRep2 DMSO_0.02pct_7d Sites epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 7 d with 0.02% Dimethyl sufloxide (DMSO) (Myers) Sites A549 DMSO 0.02% 7 d Methyl RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsA549Dm002p7dHaibSitesRep1 A549 1 A549 MethylRrbs ENCODE Mar 2012 Freeze 2011-08-31 2012-05-31 wgEncodeEH002062 2062 GSM980580 Myers HudsonAlpha SL3655 HudsonAlpha 1 wgEncodeHaibMethylRrbsA549Dm002p7dHaibSitesRep1 DMSO_0.02pct_7d Sites epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology 7 d with 0.02% Dimethyl sufloxide (DMSO) (Myers) Sites A549 DMSO 0.02% 7 d Methyl RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsK562HaibSitesRep2 K562 2 K562 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001364 1364 GSM683780 Myers HudsonAlpha SL726 HudsonAlpha 2 wgEncodeHaibMethylRrbsK562HaibSitesRep2 None Sites leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites K562 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsK562HaibSitesRep1 K562 1 K562 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001364 1364 GSM683856 Myers HudsonAlpha SL725 HudsonAlpha 1 wgEncodeHaibMethylRrbsK562HaibSitesRep1 None Sites leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites K562 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsH1hescHaibSitesRep2 H1-hESC 2 H1-hESC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001362 1362 GSM683879 Myers HudsonAlpha SL713 HudsonAlpha 2 wgEncodeHaibMethylRrbsH1hescHaibSitesRep2 None Sites embryonic stem cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites H1-hESC Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsH1hescHaibSitesRep1 H1-hESC 1 H1-hESC MethylRrbs ENCODE Jan 2011 Freeze 2010-07-16 2011-04-16 wgEncodeEH001362 1362 GSM683770 Myers HudsonAlpha SL716 HudsonAlpha 1 wgEncodeHaibMethylRrbsH1hescHaibSitesRep1 None Sites embryonic stem cells DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites H1-hESC Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12878HaibSitesRep2 GM12878 2 GM12878 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001355 1355 GSM683927 Myers HudsonAlpha SL728 HudsonAlpha 2 wgEncodeHaibMethylRrbsGm12878HaibSitesRep2 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12878 Methyl-RRBS Rep 2 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethylRrbsGm12878HaibSitesRep1 GM12878 1 GM12878 MethylRrbs ENCODE Jan 2011 Freeze 2010-07-15 2011-04-15 wgEncodeEH001355 1355 GSM683906 Myers HudsonAlpha SL727 HudsonAlpha 1 wgEncodeHaibMethylRrbsGm12878HaibSitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNA Methyl Reduced Rep Bisulfite Seq Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12878 Methyl-RRBS Rep 1 from ENCODE/HudsonAlpha Regulation 
wgEncodeHaibMethyl450 HAIB Methyl450 GSE40699 CpG Methylation by Methyl 450K  Bead Arrays from ENCODE/HAIB Regulation Description This track is produced as part of the ENCODE project. The track displays the methylation status of specific CpG dinucleotides in the given cell types as identified by the Illumina Infinium Human Methylation 450 Bead Array platform. In general, methylation of CpG sites within a promoter causes silencing of the gene associated with that promoter. The Infinium Human Methylation 450 platform uses bisulfite treated genomic DNA to assay the methylation status of more than 450,000 CpG sites covering all designatable RefSeq genes, including promoter, 5' and 3' regions, without bias against those lacking CpG islands. Additionally, the assay includes CpG islands and shores, CpG sites outside of CpG islands, non-CpG methylated sites identified in human stem cells, differentially methylated sites identified in tumor versus normal (multiple forms of cancer) and across several tissue types, CpG islands outside of coding regions, miRNA promoter regions, and disease-associated regions identified through GWAS. The detailed protocol, information for CpG targets, and beta values are available from the supplemental directory. Display Conventions and Configuration Scores associated with each site are beta values (see Methods) multiplied by 1000. Methylation status is color-coded as: orange = methylated (score &gt;= 600) purple = partially methylated (200 &lt; score &lt; 600) bright blue = unmethylated (0 &lt; score &lt;= 200) black = NA (score = 0) Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Genomic DNA was isolated from each cell line with the QIAGEN DNeasy Blood &amp; Tissue Kit according to the instructions provided by the manufacturer. DNA concentrations and a level of quality of each preparation was determined by fluorescence with the Qubit Fluorometer (Invitrogen). Genomic DNA was treated with sodium bisulfite, converting unmethylated cytosines of CpG dinucleotides into uracils; methylated cytosines did not get converted. After bisulfite treatment, the methylation status of a site was assayed by single base-pair extension with a Cy3 or Cy5 labeled nucleotide on oligo-beads specific for the methylated or unmethylated state. The bisulfite conversion reaction was done using the Zymo Research EZ-96 DNA MethylationTM Kit. One step of the protocol was modified. During the incubation, a 30 second 95oC denaturing step every hour was included to increase reaction efficiency as recommended by the Illumina Infinium Human Methylation27 protocol. The bead arrays were run according to the protocol provided by Illumina. A beta value was calculated for each CpG target with Illumina's Bead Studio software with the Methylation Module v3.2. Beta-value = intensity value from the methylated bead type/(intensity values from the methylated + intensity value from unmethylated bead types + 100). The data was then quality-filtered using p-values. Beta values with p-value greater than 0.01 are considered to fall below the minimum intensity and threshold are displayed as "NA". Any beta value equal to or greater than 0.6 was considered fully methylated. Any beta value equal to or less than 0.2 was considered to be fully unmethylated. Beta values between 0.2 and 0.6 were considered to be partially methylated. Release Notes This is Release 1 (Dec 2011) of the 450K bead array data, with data corrections applied to the displayed data tables in May 2012. A perl script to correct coordinates in the download files has been included in the download directory. The initial release had incorrect probe mappings. The data providers also requested these annotations be limited to the first nucleotide in the probe, so the single CpG assayed is displayed instead of the full probe. When the Infinium platform was first released, it was thought that methylation states of CpG's within the 50 bp window could be assigned by assaying a single nucleotide, but it has since been determined that methylation states vary even at close distances. Credits These data were produced by the Dr. Richard Myers Lab and the Dr. Devin Absher lab at the HudsonAlpha Institute for Biotechnology. Cells were grown by the Myers Lab and other ENCODE production groups. Contact: Dr. Florencia Pauli. References --> Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeHaibMethyl450U87SitesRep1 U87 U87 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002233 2233 GSM999396 Myers HudsonAlpha Methyl450K HudsonAlpha 1 F wgEncodeHaibMethyl450U87SitesRep1 None Sites glioblastoma, astrocytoma, (PMID: 4332744) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Female Sites U87 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450T47dDm002p24hSitesRep1 T-47D DMSO T-47D MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002184 2184 GSM999377 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450T47dDm002p24hSitesRep1 DMSO_0.02pct_24hr Sites epithelial cell line derived from a mammary ductal carcinoma. DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology 24 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Sites T-47D DMSO Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450SknshraSitesRep1 SK-N-SH_RA SK-N-SH_RA MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002231 2231 GSM999388 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450SknshraSitesRep1 None Sites neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-SH_RA Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450SknmcSitesRep1 SK-N-MC SK-N-MC MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002183 2183 GSM999370 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450SknmcSitesRep1 None Sites neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-MC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450SkmcSitesRep1 SKMC SKMC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002232 2232 GSM999335 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450SkmcSitesRep1 None Sites skeletal muscle cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites SKMC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450SaecSitesRep1 SAEC SAEC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002229 2229 GSM999346 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450SaecSitesRep1 None Sites small airway epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites SAEC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450RptecSitesRep1 RPTEC RPTEC MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002197 2197 GSM999343 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450RptecSitesRep1 None Sites renal proximal tubule epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites RPTEC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450ProgfibSitesRep1 ProgFib ProgFib MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002196 2196 GSM999342 Myers HudsonAlpha Methyl450K Duke 1 wgEncodeHaibMethyl450ProgfibSitesRep1 None Sites fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites ProgFib Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450PrecSitesRep1 PrEC PrEC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002228 2228 GSM999369 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450PrecSitesRep1 None Sites prostate epithelial cell line DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites PrEC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Pfsk1SitesRep1 PFSK-1 PFSK-1 MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002182 2182 GSM999371 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Pfsk1SitesRep1 None Sites neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites PFSK-1 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Panc1SitesRep1 PANC-1 PANC-1 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002227 2227 GSM999395 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Panc1SitesRep1 None Sites pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites PANC-1 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ovcar3SitesRep1 ovcar-3 ovcar-3 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002234 2234 GSM999393 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Ovcar3SitesRep1 None Sites ovarian adenocarcinoma, "the NIH: OVCAR-3 line was established in 1982 by T.C. Hamilton, et al. from the malignant ascites of a patient with progressive adenocarcinoma of the ovary." - ATCC. (PMID: 6604576) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites ovcar-3 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Nt2d1SitesRep1 NT2-D1 NT2-D1 MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002181 2181 GSM999372 Myers HudsonAlpha Methyl450K Stanford 1 wgEncodeHaibMethyl450Nt2d1SitesRep1 None Sites malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites NT2-D1 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450NhdfneoSitesRep1 NHDF-neo NHDF-neo MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002226 2226 GSM999394 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450NhdfneoSitesRep1 None Sites neonatal dermal fibroblasts DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites NHDF-neo Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450NhbeSitesRep1 NHBE NHBE MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002225 2225 GSM999358 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450NhbeSitesRep1 None Sites bronchial epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites NHBE Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450NhaSitesRep1 NH-A NH-A MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002224 2224 GSM999357 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450NhaSitesRep1 None Sites astrocytes (also called Astrocy) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites NH-A Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Nb4SitesRep1 NB4 NB4 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002223 2223 GSM999360 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Nb4SitesRep1 None Sites acute promyelocytic leukemia cell line. (PMID: 1995093) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites NB4 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Mcf10aesSitesRep1 MCF10A MCF10A-Er-Src MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002222 2222 GSM999359 Myers HudsonAlpha Methyl450K Stanford 1 wgEncodeHaibMethyl450Mcf10aesSitesRep1 None Sites mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites MCF10A Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Mcf10aesTamSitesRep1 MCF10A TAM MCF10A-Er-Src MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002235 2235 GSM999392 Myers HudsonAlpha Methyl450K Stanford 1 wgEncodeHaibMethyl450Mcf10aesTamSitesRep1 4OHTAM_1uM_36hr Sites mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Sites MCF10A TAM Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450LncapSitesRep1 LNCaP LNCaP MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002179 2179 GSM999368 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450LncapSitesRep1 None Sites prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites LNCaP Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450JurkatSitesRep1 Jurkat Jurkat MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002178 2178 GSM999367 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450JurkatSitesRep1 None Sites T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites Jurkat Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HrpeSitesRep1 HRPEpiC HRPEpiC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002221 2221 GSM999362 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HrpeSitesRep1 None Sites retinal pigment epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRPEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HreSitesRep1 HRE HRE MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002220 2220 GSM999361 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HreSitesRep1 None Sites renal epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRE Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HrceSitesRep1 HRCEpiC HRCEpiC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002219 2219 GSM999390 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HrceSitesRep1 None Sites renal cortical epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HRCEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HpaeSitesRep1 HPAEpiC HPAEpiC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002218 2218 GSM999391 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HpaeSitesRep1 None Sites pulmonary alveolar epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HPAEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HnpceSitesRep1 HNPCEpiC HNPCEpiC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002217 2217 GSM999384 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HnpceSitesRep1 None Sites non-pigment ciliary epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HNPCEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HmecSitesRep1 HMEC HMEC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002216 2216 GSM999385 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HmecSitesRep1 None Sites mammary epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HMEC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Hl60SitesRep1 HL-60 HL-60 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002215 2215 GSM999386 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Hl60SitesRep1 None Sites promyelocytic leukemia cells, (PMID: 276884) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HL-60 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HipeSitesRep1 HIPEpiC HIPEpiC MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002190 2190 GSM999336 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HipeSitesRep1 None Sites iris pigment epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HIPEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HepatoSitesRep1 Hepatocyte Hepatocytes MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002193 2193 GSM999339 Myers HudsonAlpha Methyl450K Duke 1 wgEncodeHaibMethyl450HepatoSitesRep1 None Sites primary hepatocytes, liver perfused by enzymes to generate single cell suspension DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites Hepatocyte Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Hek293SitesRep1 HEK293 HEK293 MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002176 2176 GSM999363 Myers HudsonAlpha Methyl450K Stanford 1 wgEncodeHaibMethyl450Hek293SitesRep1 None Sites embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEK293 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HeeSitesRep1 HEEpiC HEEpiC MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002189 2189 GSM999378 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HeeSitesRep1 None Sites esophageal epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HEEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Hct116StanfordSitesRep1 HCT-116 Stanford HCT-116 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002214 2214 GSM999387 Myers HudsonAlpha Methyl450K Stanford 1 wgEncodeHaibMethyl450Hct116StanfordSitesRep1 None Sites colorectal carcinoma (PMID: 7214343) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCT-116 Stanford Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Hct116HaibSitesRep1 HCT-116 HAIB HCT-116 MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002214 2214 GSM999387 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Hct116HaibSitesRep1 None Sites colorectal carcinoma (PMID: 7214343) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCT-116 HAIB Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HcpeSitesRep1 HCPEpiC HCPEpiC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002213 2213 GSM999380 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HcpeSitesRep1 None Sites choroid plexus epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCPEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HcmSitesRep1 HCM HCM MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002212 2212 GSM999381 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HcmSitesRep1 None Sites cardiac myocytes DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCM Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HcfSitesRep1 HCF HCF MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002211 2211 GSM999382 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HcfSitesRep1 None Sites cardiac fibroblasts DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HCF Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HaeSitesRep1 HAEpiC HAEpiC MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002208 2208 GSM999355 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450HaeSitesRep1 None Sites amniotic epithelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HAEpiC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Gm19239SitesRep1 GM19239 GM19239 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002207 2207 GSM999354 Myers HudsonAlpha Methyl450K Duke 1 wgEncodeHaibMethyl450Gm19239SitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM19239 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Gm12892SitesRep1 GM12892 GM12892 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002187 2187 GSM999374 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Gm12892SitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12892 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Gm12891SitesRep1 GM12891 GM12891 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002186 2186 GSM999375 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Gm12891SitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12891 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Gm06990SitesRep1 GM06990 GM06990 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002206 2206 GSM999353 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Gm06990SitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM06990 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ecc1SitesRep1 ECC-1 ECC-1 MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002175 2175 GSM999366 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Ecc1SitesRep1 None Sites epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites ECC-1 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450CmkSitesRep1 CMK CMK MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002204 2204 GSM999351 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450CmkSitesRep1 None Sites acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites CMK Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Caco2SitesRep1 Caco-2 Caco-2 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002205 2205 GSM999352 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Caco2SitesRep1 None Sites colorectal adenocarcinoma. (PMID: 1939345) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites Caco-2 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450BjSitesRep1 BJ BJ MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002203 2203 GSM999350 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450BjSitesRep1 None Sites skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites BJ Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Be2cSitesRep1 BE2_C BE2_C MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002210 2210 GSM999383 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Be2cSitesRep1 None Sites neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites BE2_C Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450AosmcSitesRep1 AoSMC AoSMC MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002209 2209 GSM999356 Myers HudsonAlpha Methyl450K Duke 1 wgEncodeHaibMethyl450AosmcSitesRep1 None Sites aortic smooth muscle cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites AoSMC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ag10803SitesRep1 AG10803 AG10803 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002202 2202 GSM999349 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Ag10803SitesRep1 None Sites abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG10803 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ag09319SitesRep1 AG09319 AG09319 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002201 2201 GSM999348 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Ag09319SitesRep1 None Sites gum tissue fibroblasts from apparently heathly 24 year old DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG09319 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ag09309SitesRep1 AG09309 AG09309 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002200 2200 GSM999347 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Ag09309SitesRep1 None Sites adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG09309 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ag04450SitesRep1 AG04450 AG04450 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002199 2199 GSM999345 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Ag04450SitesRep1 None Sites fetal lung fibroblast DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG04450 Methylation  450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Ag04449SitesRep1 AG04449 AG04449 MethylArray ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002198 2198 GSM999344 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Ag04449SitesRep1 None Sites fetal buttock/thigh fibroblast DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites AG04449 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450SknshSitesRep1 SK-N-SH SK-N-SH MethylArray ENCODE Mar 2012 Freeze 2011-10-01 2012-06-30 wgEncodeEH002230 2230 GSM999389 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450SknshSitesRep1 None Sites neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites SK-N-SH Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Mcf7SitesRep1 MCF-7 MCF-7 MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002180 2180 GSM999373 Myers HudsonAlpha Methyl450K Duke 1 wgEncodeHaibMethyl450Mcf7SitesRep1 None Sites mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites MCF-7 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Imr90SitesRep1 IMR90 IMR90 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002194 2194 GSM999340 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Imr90SitesRep1 None Sites fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites IMR90 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450HuvecSitesRep1 HUVEC HUVEC MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002177 2177 GSM999364 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450HuvecSitesRep1 None Sites umbilical vein endothelial cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HUVEC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Hepg2SitesRep1 HepG2 HepG2 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002192 2192 GSM999338 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Hepg2SitesRep1 None Sites hepatocellular carcinoma DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HepG2 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Helas3SitesRep1 HeLa-S3 HeLa-S3 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002191 2191 GSM999337 Myers HudsonAlpha Methyl450K UW 1 wgEncodeHaibMethyl450Helas3SitesRep1 None Sites cervical carcinoma DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites HeLa-S3 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450A549Etoh02SitesRep1 A549 ETOH A549 MethylArray ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002174 2174 GSM999365 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450A549Etoh02SitesRep1 EtOH_0.02pct Sites epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology 1 h with 0.02% Ethanol (Myers) Sites A549 EtOH Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450K562SitesRep1 K562 K562 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002195 2195 GSM999341 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450K562SitesRep1 None Sites leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites K562 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450H1hescSitesRep1 H1-hESC H1-hESC MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002188 2188 GSM999379 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450H1hescSitesRep1 None Sites embryonic stem cells DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites H1-hESC Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibMethyl450Gm12878SitesRep1 GM12878 GM12878 MethylArray ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002185 2185 GSM999376 Myers HudsonAlpha Methyl450K HudsonAlpha 1 wgEncodeHaibMethyl450Gm12878SitesRep1 None Sites B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus DNA Methylation Array Myers Myers - Hudson Alpha Institute for Biotechnology Sites GM12878 Methylation 450K Bead Array from ENCODE/HAIB Regulation 
wgEncodeHaibRnaSeq HAIB RNA-seq GSE35584 RNA-seq from ENCODE/HAIB Expression Description This track was produced as part of the ENCODE Project. RNA-seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly (Mortazavi et al., 2008). Biological replicates of ENCODE cell lines were grown on separate culture plates, total RNA was purified and polyA selected two times. The mRNA extract was then fragmented by magnesium-catalyzed hydrolysis and reverse transcribed to cDNA by random priming and amplification. The cDNA was sequenced on an Illumina Genome Analyzer (GAI or GAIIx). The DNA sequences were aligned to the NCBI Build37 (hg19) version of the human genome using the sequence alignment programs ELAND (Illumina) or Bowtie (Langmead et al., 2009). The first 10 residues of sequencing have a weak characteristic nucleotide bias of unknown origin. This RNA-seq protocol does not specify the coding strand. As a result, there will be ambiguity at loci where both strands are transcribed. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks (cell lines, replicates and growth conditions) that display individually on the browser. Instructions for configuring multi-view tracks are here. The following views are in this track: Alignments The Alignments view shows reads mapped to the genome. See the Bowtie Manual for more information about the SAM Bowtie output (including tag definitions) and the SAM Format Specification for more information on the SAM/BAM file format. The reads are named using the following convention: Lane &#35;:Tile &#35;:X-coordinate:Y-coordinate Raw Signal Density graph of signal enrichment based on a normalized aligned read density (Read Per Million, RPM). RPM is reported in the score field and is equal to the number of reads at that position divided by the total number of reads divided by one million. The Raw Signal view displays dense, continuous data as a graph and the RPM measure assists in visualizing the relative amount of a given transcript across multiple samples. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Experimental Procedures Cells were grown according to the approved ENCODE cell culture protocols. Cells were lysed in RLT buffer (Qiagen RNEasy kit) and processed on RNEasy midi columns according to the manufacturer's protocol, with the inclusion of the "on-column" DNase digestion step to remove residual genomic DNA. The mRNA was isolated from at least 10 ug of total RNA with oligo(dT) two times (Dynabeads mRNA PurificationgKit, Invitrogen). Alternatively, cells were lysed and mRNA was purified directly two times with oligo(dT) (Dynabeads mRNA DIRECT Kit, Invitrogen). A quantity of 100 ng of mRNA was fragmented by magnesium-catalyzed hydrolysis and reverse transcribed to cDNA by random priming according to the protocol in Mortazavi et al. (2008). The cDNA was prepared for sequencing on the Genome Analyzer flowcell according to the protocol for the ChIPSeq DNA genomic DNA kit (Illumina). The sequencing libraries were size-selected around 225 bp and amplified with 15 rounds of PCR. Libraries were sequenced with an Illumina Genome Analyzer I or an Illumina Genome Analyzer IIx according to the manufacturer's recommendations. Single end reads of 36 nt in length were obtained. Data Processing and Analysis FastQ files were made from qseq files generated by the Illumina pipeline (Casava 1.7). The Raw Signal files (bigWig) were generated from bedgraph files and the score was calculated as the number of reads at that position divided by the total number of reads divided by one million. Casava export files were aligned to the NCBI Build37 (hg19) version of the human genome with ELAND (Illumina), generating SAM files. FastQ files of experiments that were previously aligned to NCBI Build36 (hg18) were aligned to NCBI Build37 (hg19) using Bowtie (Langmead et al., 2009; parameters: -S -n 2 -k 11 -m 10 --best), also generating SAM files. SAM files were converted to BAM files with SAMtools (Li et al., 2009). Gene expression within GENCODE V7 (Harrow et al., 2006) gene models was estimated using Cufflinks v0.9.3 (Roberts et al., 2011). Estimates of transcript abundance were reported in Fragments Per Kilobase of exon per Million fragments mapped (FPKM). FPKM is calculated by dividing the total number of fragments that align to the gene model by the size of the spliced transcript (exons) in kilobases. This number is then divided by the total number of reads in millions for the experiment. FPKM is reported in the last column of the GTF (TranscriptGencV7) files. Raw Data (fastQ), Raw Signal (bigWig), Alignments (BAM) and Transcript GENCODE V7 (GTF) files are available from the Downloads page. Verification The mapped data were visually inspected to verify the majority of the reads fell within known exons. Biological replicates confirm expression measurements with r &gt; 0.90. Release Notes Update (May 2012): the labels of the Raw Signal subtracks have been updated because they were originally labeled as Signals instead of Raw Signals. This is the first NCBI Build37 (hg19) release of this track (Feb 2012). This release includes the 3 datasets (Jurkat, A549/DEX100nm, and A549/EtOH2pct) previously released on NCBI Build36 (hg18) and adds data for several more cell types and growth conditions in replicate. Four types of download files are available for each replicate including the Raw Data (fastQ), Transcript GENCODE V7 (GTF), Raw Signal (bigWig), and Alignments (BAM). Credits These data were produced by the Dr. Richard Myers Lab at the HudsonAlpha Institute for Biotechnology. Contact: Dr. Florencia Pauli References Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7 Suppl 1:S4.1-9. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8. Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol. 2011;12(3):R22. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeHaibRnaSeqViewSignal Signal RNA-seq from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqU87RawRep2V2 U87 2 U87 RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-09 wgEncodeEH001253 1253 GSM923437 Myers HudsonAlpha SL533 cufflinks_v_0.9 bow125 hg18 1x36 2 longPolyA wgEncodeHaibRnaSeqU87RawRep2V2 None RawSignal glioblastoma, astrocytoma, (PMID: 4332744) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqU87RawRep1V2 U87 1 U87 RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-09 wgEncodeEH001253 1253 GSM923437 Myers HudsonAlpha SL532 cufflinks_v_0.9 bow125 hg18 1x36 1 longPolyA wgEncodeHaibRnaSeqU87RawRep1V2 None RawSignal glioblastoma, astrocytoma, (PMID: 4332744) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dGen4hRawRep2 T-47D GEN 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001245 1245 GSM923436 Myers HudsonAlpha SL1549 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dGen4hRawRep2 Genistein_100nM_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D GENISTEIN 4 hr 100 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dGen4hRawRep1 T-47D GEN 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001245 1245 GSM923436 Myers HudsonAlpha SL1246 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dGen4hRawRep1 Genistein_100nM_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D GENISTEIN 4 hr 100 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dEstradia4hRawRep2 T-47D EST 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001244 1244 GSM923431 Myers HudsonAlpha SL1548 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dEstradia4hRawRep2 Estradiol_10nM_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ESTRADIOL 4 hr 10 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dEstradia4hRawRep1 T-47D EST 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001244 1244 GSM923431 Myers HudsonAlpha SL1245 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dEstradia4hRawRep1 Estradiol_10nM_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ESTRADIOL 4 hr 10 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dDm002p4hRawRep2 T-47D DMSO 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001243 1243 GSM923428 Myers HudsonAlpha SL1547 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dDm002p4hRawRep2 DMSO_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D DMSO 4 hr 0.02% RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dDm002p4hRawRep1 T-47D DMSO 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001243 1243 GSM923428 Myers HudsonAlpha SL1244 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dDm002p4hRawRep1 DMSO_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D DMSO 4 hr 0.02% RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dBpa14hRawRep2 T-47D BPA 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001242 1242 GSM923429 Myers HudsonAlpha SL1911 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dBpa14hRawRep2 BPA_100nM_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D BPA 4 hr 100 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dBpa14hRawRep1 T-47D BPA 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001242 1242 GSM923429 Myers HudsonAlpha SL1550 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dBpa14hRawRep1 BPA_100nM_4hr RawSignal epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D BPA 4 hr 100 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPfsk1RawRep2 PFSK-1 2 PFSK-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001252 1252 GSM923430 Myers HudsonAlpha SL531 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqPfsk1RawRep2 None RawSignal neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPfsk1RawRep1 PFSK-1 1 PFSK-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001252 1252 GSM923430 Myers HudsonAlpha SL530 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqPfsk1RawRep1 None RawSignal neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPanc1RawRep2 PANC-1 2 PANC-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001251 1251 GSM923421 Myers HudsonAlpha SL529 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqPanc1RawRep2 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPanc1RawRep1 PANC-1 1 PANC-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001251 1251 GSM923421 Myers HudsonAlpha SL528 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqPanc1RawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqJurkatRawRep2 Jurkat 2 Jurkat RnaSeq ENCODE Mar 2012 Freeze 2011-04-05 2012-01-04 wgEncodeEH000315 315 GSM923424 Myers HudsonAlpha SL317 cufflinks_v_0.9 bow125 hg18 1x36 2 longPolyA wgEncodeHaibRnaSeqJurkatRawRep2 None RawSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqJurkatRawRep1 Jurkat 1 Jurkat RnaSeq ENCODE Mar 2012 Freeze 2012-01-24 2012-10-24 wgEncodeEH000315 315 GSM923424 Myers HudsonAlpha SL316 cufflinks_v_0.9 bow125 hg18 1x36 1 longPolyA wgEncodeHaibRnaSeqJurkatRawRep1 None RawSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Gen4hRawRep2 ECC-1 GEN 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001241 1241 GSM923426 Myers HudsonAlpha SL2860 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Gen4hRawRep2 Genistein_100nM_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 GENISTEIN 4 hr 100 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Gen4hRawRep1 ECC-1 GEN 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001241 1241 GSM923426 Myers HudsonAlpha SL991 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Gen4hRawRep1 Genistein_100nM_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 GENISTEIN 4 hr 100 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Estradia4hRawRep2 ECC-1 EST 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001240 1240 GSM923427 Myers HudsonAlpha SL2932 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Estradia4hRawRep2 Estradiol_10nM_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ESTRADIOL 4 hr 10 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Estradia4hRawRep1 ECC-1 EST 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001240 1240 GSM923427 Myers HudsonAlpha SL990 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Estradia4hRawRep1 Estradiol_10nM_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ESTRADIOL 4 hr 10 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Dm002p4hRawRep2 ECC-1 DMSO 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001239 1239 GSM923423 Myers HudsonAlpha SL2861 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Dm002p4hRawRep2 DMSO_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 DMSO 4 hr 0.02% RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Dm002p4hRawRep1 ECC-1 DMSO 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001239 1239 GSM923423 Myers HudsonAlpha SL989 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Dm002p4hRawRep1 DMSO_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 DMSO 4 hr 0.02% RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Bpa14hRawRep2 ECC-1 BPA 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001238 1238 GSM923422 Myers HudsonAlpha SL2859 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Bpa14hRawRep2 BPA_100nM_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 BPA 4 hr 100 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Bpa14hRawRep1 ECC-1 BPA 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001238 1238 GSM923422 Myers HudsonAlpha SL1552 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Bpa14hRawRep1 BPA_100nM_4hr RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 BPA 4 hr 100 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqBe2cRawRep2 BE2_C 2 BE2_C RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001249 1249 GSM923434 Myers HudsonAlpha SL525 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqBe2cRawRep2 None RawSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2_C RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqBe2cRawRep1 BE2_C 1 BE2_C RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001249 1249 GSM923434 Myers HudsonAlpha SL524 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqBe2cRawRep1 None RawSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2_C RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqSknshRawRep2 SK-N-SH 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001250 1250 GSM923419 Myers HudsonAlpha SL527 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqSknshRawRep2 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqSknshRawRep1 SK-N-SH 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001250 1250 GSM923419 Myers HudsonAlpha SL526 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqSknshRawRep1 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02RawRep4 A549 ETOH 4 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000314 314 GSM923425 Myers HudsonAlpha SL1260 cufflinks_v_0.9 bow125 hg19 1x36 4 longPolyA wgEncodeHaibRnaSeqA549Etoh02RawRep4 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ETOH 1 hr 0.02% RNA-seq Raw Signal Rep 4 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02RawRep3 A549 ETOH 3 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000314 314 GSM923425 Myers HudsonAlpha SL1255 cufflinks_v_0.9 bow125 hg19 1x36 3 longPolyA wgEncodeHaibRnaSeqA549Etoh02RawRep3 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ETOH 1 hr 0.02% RNA-seq Raw Signal Rep 3 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02RawRep2 A549 ETOH 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000314 314 GSM923425 Myers HudsonAlpha SL333 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Etoh02RawRep2 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ETOH 1 hr 0.02% RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02RawRep1 A549 ETOH 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000314 314 GSM923425 Myers HudsonAlpha SL331 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Etoh02RawRep1 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ETOH 1 hr 0.02% RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex5nmRawRep2 A549 DEX5nM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001248 1248 GSM923435 Myers HudsonAlpha SL1264 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex5nmRawRep2 DEX_5nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 5 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 5 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex5nmRawRep1 A549 DEX5nM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001248 1248 GSM923435 Myers HudsonAlpha SL1259 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex5nmRawRep1 DEX_5nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 5 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 5 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex500pmRawRep2 A549 DEX500pM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001247 1247 GSM923432 Myers HudsonAlpha SL1262 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex500pmRawRep2 DEX_500pM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 500 pM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 500 pM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex500pmRawRep1 A549 DEX500pM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001247 1247 GSM923432 Myers HudsonAlpha SL1257 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex500pmRawRep1 DEX_500pM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 500 pM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 500 pM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex1nmRawRep2 A549 DEX1nM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001246 1246 GSM923433 Myers HudsonAlpha SL1263 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex1nmRawRep2 DEX_1nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 1 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 1 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex1nmRawRep1 A549 DEX1nM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001246 1246 GSM923433 Myers HudsonAlpha SL1258 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex1nmRawRep1 DEX_1nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 1 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 1 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100pmRawRep2 A549 DEX100pM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001237 1237 GSM923418 Myers HudsonAlpha SL1261 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex100pmRawRep2 DEX_100pM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 pM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 100 pM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100pmRawRep1 A549 DEX100pM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001237 1237 GSM923418 Myers HudsonAlpha SL1256 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex100pmRawRep1 DEX_100pM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 pM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 100 pM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100nmRawRep2 A549 DEX100nM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000313 313 GSM923420 Myers HudsonAlpha SL332 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex100nmRawRep2 DEX_100nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 100 nM RNA-seq Raw Signal Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100nmRawRep1 A549 DEX100nM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000313 313 GSM923420 Myers HudsonAlpha SL330 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex100nmRawRep1 DEX_100nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 DEX 1 hr 100 nM RNA-seq Raw Signal Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqViewAlignments Alignments RNA-seq from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqU87AlnRep2V2 U87 2 U87 RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-09 wgEncodeEH001253 1253 Myers HudsonAlpha SL533 cufflinks_v_0.9 bow125 hg18 1x36 2 longPolyA wgEncodeHaibRnaSeqU87AlnRep2V2 None Alignments glioblastoma, astrocytoma, (PMID: 4332744) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch U87 RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqU87AlnRep1V2 U87 1 U87 RnaSeq ENCODE Mar 2012 Freeze 2012-02-10 2012-11-09 wgEncodeEH001253 1253 Myers HudsonAlpha SL532 cufflinks_v_0.9 bow125 hg18 1x36 1 longPolyA wgEncodeHaibRnaSeqU87AlnRep1V2 None Alignments glioblastoma, astrocytoma, (PMID: 4332744) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch U87 RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dGen4hAlnRep2 T-47D GEN 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001245 1245 Myers HudsonAlpha SL1549 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dGen4hAlnRep2 Genistein_100nM_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D GENISTEIN 4 hr 100 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dGen4hAlnRep1 T-47D GEN 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001245 1245 Myers HudsonAlpha SL1246 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dGen4hAlnRep1 Genistein_100nM_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D GENISTEIN 4 hr 100 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dEstradia4hAlnRep2 T-47D EST 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001244 1244 Myers HudsonAlpha SL1548 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dEstradia4hAlnRep2 Estradiol_10nM_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D ESTRADIOL 4 hr 10 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dEstradia4hAlnRep1 T-47D EST 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001244 1244 Myers HudsonAlpha SL1245 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dEstradia4hAlnRep1 Estradiol_10nM_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D ESTRADIOL 4 hr 10 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dDm002p4hAlnRep2 T-47D DMSO 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001243 1243 Myers HudsonAlpha SL1547 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dDm002p4hAlnRep2 DMSO_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D DMSO 4 hr 0.02% RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dDm002p4hAlnRep1 T-47D DMSO 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001243 1243 Myers HudsonAlpha SL1244 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dDm002p4hAlnRep1 DMSO_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D DMSO 4 hr 0.02% RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dBpa14hAlnRep2 T-47D BPA 2 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001242 1242 Myers HudsonAlpha SL1911 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqT47dBpa14hAlnRep2 BPA_100nM_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D BPA 4 hr 100 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqT47dBpa14hAlnRep1 T-47D BPA 1 T-47D RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001242 1242 Myers HudsonAlpha SL1550 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqT47dBpa14hAlnRep1 BPA_100nM_4hr Alignments epithelial cell line derived from a mammary ductal carcinoma. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch T-47D BPA 4 hr 100 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPfsk1AlnRep2 PFSK-1 2 PFSK-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001252 1252 Myers HudsonAlpha SL531 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqPfsk1AlnRep2 None Alignments neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch PFSK-1 RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPfsk1AlnRep1 PFSK-1 1 PFSK-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001252 1252 Myers HudsonAlpha SL530 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqPfsk1AlnRep1 None Alignments neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch PFSK-1 RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPanc1AlnRep2 PANC-1 2 PANC-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001251 1251 Myers HudsonAlpha SL529 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqPanc1AlnRep2 None Alignments pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch PANC-1 RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqPanc1AlnRep1 PANC-1 1 PANC-1 RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001251 1251 Myers HudsonAlpha SL528 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqPanc1AlnRep1 None Alignments pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch PANC-1 RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqJurkatAlnRep2 Jurkat 2 Jurkat RnaSeq ENCODE Mar 2012 Freeze 2011-04-05 2012-01-04 wgEncodeEH000315 315 Myers HudsonAlpha SL317 cufflinks_v_0.9 bow125 hg18 1x36 2 longPolyA wgEncodeHaibRnaSeqJurkatAlnRep2 None Alignments T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch Jurkat RNA-seq Alignments Replicate 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqJurkatAlnRep1V2 Jurkat 1 Jurkat RnaSeq ENCODE Mar 2012 Freeze 2012-01-24 2012-10-24 wgEncodeEH000315 315 Myers HudsonAlpha SL316 cufflinks_v_0.9 bow125 hg18 1x36 1 longPolyA wgEncodeHaibRnaSeqJurkatAlnRep1V2 None Alignments T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch Jurkat RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Gen4hAlnRep2 ECC-1 GEN 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001241 1241 Myers HudsonAlpha SL2860 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Gen4hAlnRep2 Genistein_100nM_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 GENISTEIN 4 hr 100 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Gen4hAlnRep1 ECC-1 GEN 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001241 1241 Myers HudsonAlpha SL991 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Gen4hAlnRep1 Genistein_100nM_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Genistein (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 GENISTEIN 4 hr 100 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Estradia4hAlnRep2 ECC-1 EST 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001240 1240 Myers HudsonAlpha SL2932 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Estradia4hAlnRep2 Estradiol_10nM_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 ESTRADIOL 4 hr 10 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Estradia4hAlnRep1 ECC-1 EST 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001240 1240 Myers HudsonAlpha SL990 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Estradia4hAlnRep1 Estradiol_10nM_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 10 nM Estradiol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 ESTRADIOL 4 hr 10 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Dm002p4hAlnRep2 ECC-1 DMSO 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001239 1239 Myers HudsonAlpha SL2861 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Dm002p4hAlnRep2 DMSO_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 DMSO 4 hr 0.02% RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Dm002p4hAlnRep1 ECC-1 DMSO 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001239 1239 Myers HudsonAlpha SL989 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Dm002p4hAlnRep1 DMSO_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 hr with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 DMSO 4 hr 0.02% RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Bpa14hAlnRep2 ECC-1 BPA 2 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001238 1238 Myers HudsonAlpha SL2859 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqEcc1Bpa14hAlnRep2 BPA_100nM_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 BPA 4 hr 100 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqEcc1Bpa14hAlnRep1 ECC-1 BPA 1 ECC-1 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001238 1238 Myers HudsonAlpha SL1552 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqEcc1Bpa14hAlnRep1 BPA_100nM_4hr Alignments epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 4 h with 100 nM Bisphenol A (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch ECC-1 BPA 4 hr 100 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqBe2cAlnRep2 BE2_C 2 BE2_C RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001249 1249 Myers HudsonAlpha SL525 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqBe2cAlnRep2 None Alignments neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch BE2_C RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqBe2cAlnRep1 BE2_C 1 BE2_C RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001249 1249 Myers HudsonAlpha SL524 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqBe2cAlnRep1 None Alignments neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch BE2_C RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqSknshAlnRep2 SK-N-SH 2 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001250 1250 Myers HudsonAlpha SL527 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqSknshAlnRep2 None Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqSknshAlnRep1 SK-N-SH 1 SK-N-SH RnaSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001250 1250 Myers HudsonAlpha SL526 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqSknshAlnRep1 None Alignments neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt Shows individual reads mapped to the genome and indicates where bases may mismatch SK-N-SH RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02AlnRep4 A549 ETOH 4 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000314 314 Myers HudsonAlpha SL1260 cufflinks_v_0.9 bow125 hg19 1x36 4 longPolyA wgEncodeHaibRnaSeqA549Etoh02AlnRep4 EtOH_0.02pct Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 ETOH 1 hr 0.02% RNA-seq Alignments Rep 4 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02AlnRep3 A549 ETOH 3 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH000314 314 Myers HudsonAlpha SL1255 cufflinks_v_0.9 bow125 hg19 1x36 3 longPolyA wgEncodeHaibRnaSeqA549Etoh02AlnRep3 EtOH_0.02pct Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 ETOH 1 hr 0.02% RNA-seq Alignments Rep 3 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02AlnRep2 A549 ETOH 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000314 314 Myers HudsonAlpha SL333 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Etoh02AlnRep2 EtOH_0.02pct Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 ETOH 1 hr 0.02% RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Etoh02AlnRep1 A549 ETOH 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000314 314 Myers HudsonAlpha SL331 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Etoh02AlnRep1 EtOH_0.02pct Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 0.02% Ethanol (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 ETOH 1 hr 0.02% RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex5nmAlnRep2 A549 DEX5nM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001248 1248 Myers HudsonAlpha SL1264 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex5nmAlnRep2 DEX_5nM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 5 nM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 5 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex5nmAlnRep1 A549 DEX5nM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001248 1248 Myers HudsonAlpha SL1259 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex5nmAlnRep1 DEX_5nM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 5 nM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 5 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex500pmAlnRep2 A549 DEX500pM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001247 1247 Myers HudsonAlpha SL1262 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex500pmAlnRep2 DEX_500pM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 500 pM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 500 pM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex500pmAlnRep1 A549 DEX500pM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001247 1247 Myers HudsonAlpha SL1257 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex500pmAlnRep1 DEX_500pM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 500 pM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 500 pM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex1nmAlnRep2 A549 DEX1nM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001246 1246 Myers HudsonAlpha SL1263 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex1nmAlnRep2 DEX_1nM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 1 nM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 1 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex1nmAlnRep1 A549 DEX1nM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001246 1246 Myers HudsonAlpha SL1258 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex1nmAlnRep1 DEX_1nM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 1 nM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 1 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100pmAlnRep2 A549 DEX100pM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001237 1237 Myers HudsonAlpha SL1261 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex100pmAlnRep2 DEX_100pM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 pM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 100 pM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100pmAlnRep1 A549 DEX100pM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-22 2011-10-21 wgEncodeEH001237 1237 Myers HudsonAlpha SL1256 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex100pmAlnRep1 DEX_100pM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 pM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 100 pM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100nmAlnRep2 A549 DEX100nM 2 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000313 313 Myers HudsonAlpha SL332 cufflinks_v_0.9 bow125 hg19 1x36 2 longPolyA wgEncodeHaibRnaSeqA549Dex100nmAlnRep2 DEX_100nM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 nM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 100 nM RNA-seq Alignments Rep 2 from ENCODE/HAIB Expression 
wgEncodeHaibRnaSeqA549Dex100nmAlnRep1 A549 DEX100nM 1 A549 RnaSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH000313 313 Myers HudsonAlpha SL330 cufflinks_v_0.9 bow125 hg19 1x36 1 longPolyA wgEncodeHaibRnaSeqA549Dex100nmAlnRep1 DEX_100nM Alignments epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Sequencing analysis of RNA expression Myers Myers - Hudson Alpha Institute for Biotechnology bowtie v0.12.5 Single 36 nt reads Poly(A)+ RNA longer than 200 nt 1 h with 100 nM Dexamethasone (Myers) Shows individual reads mapped to the genome and indicates where bases may mismatch A549 DEX 1 hr 100 nM RNA-seq Alignments Rep 1 from ENCODE/HAIB Expression 
wgEncodeHaibTfbs HAIB TFBS GSE32465 Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB Regulation Description This track displays binding sites of the specified transcription factors in the given cell types as identified by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq &mdash; see Johnson et al., 2007 and Fields, 2007). ChIP-seq was used to assay chromatin fragments bound by specific or general transcription factors as described below. DNA enriched by chromatin immunoprecipitation was sequenced and short sequence reads of 25-36 nt were mapped to the human reference genome. Enriched regions (peaks) of high sequence read density relative to input chromatin control sequence reads were identified with a peak calling algorithm. The sequence reads with quality scores (fastq files) and alignment coordinates (BAM files) from these experiments are available for download. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. The subtracks in this track are grouped by transcription factor targeted antibody and by cell type. For each experiment (cell type vs. antibody), the following views are included: Peaks Sites with the greatest evidence of transcription factor binding, calculated using the MACS peak caller (Zhang et al., 2008), as enriched regions of high read density in the ChIP experiment relative to total input chromatin control reads. Raw Signal A continuous signal which indicates density of aligned reads. The sequence reads were extended to the size-selected length (225 bp), and the read density computed as reads per million. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Cross-linked chromatin was immunoprecipitated with an antibody, the protein-DNA crosslinks were reversed and the DNA fragments were recovered and sequenced. Please see protocol notes below and check here for the most current version of the protocol. Biological replicates from each experiment were completed. Libraries were sequenced with an Illumina Genome Analyzer I or IIx according to the manufacturer's recommendations. Sequence data produced by the Illumina data pipeline software were quality-filtered and then mapped to NCBI GRCh37 (hg19) using the integrated Eland software; 32 nt of the sequence reads were used for alignment. Up to two mismatches were tolerated; reads that mapped to multiple sites in the genome were discarded. To identify likely transcription factor occupancy sites, peak calling was applied to the aligned sequence data sets using MACS (Zhang et al., 2008). The MACS method models the shift size of ChIP-seq tags empirically, and uses the shift to improve the spatial resolution of predicted binding sites. The MACS method also uses a dynamic Poisson distribution to capture local biases in the genome, allowing for more robust predictions (Zhang et al., 2008). Protocol Notes Several changes and improvements were made to the original ChIP-seq protocol (Jonshon et al., 2008). The major differences between protocols are the number of cells and magnetic beads used for IP, the method of sonication used to fragment DNA, the method used for fragment size selection, and the number of cycles of PCR used to amplify the sequencing library. The protocol field for each file denotes the version of the protocol used as being PCR1x, PCR2x or a version number (e.g., v041610.1). The sequencing libraries labeled as PCR2x were made with two rounds of amplification (25 and 15 cycles) and those labeled as PCR1x were made with one 15-cycle round of amplification. Experiments that were completed prior to January 2010 were originally aligned to NCBI36 (hg18). They have been re-aligned to NCBI GRCh37 (hg19) with the Bowtie software (Langmead et al., 2009) for this data release. The libraries labeled with a protocol version number were competed after January 2010 and were only aligned to NCBI GRCh37 (hg19). Please refer to the Myers Lab website for details on each protocol version and the most current protocol in use. Verification The MACS peak caller was used to call significant peaks on the individual replicates of a ChIP-seq experiment. Next, the irreproducible discovery rate (IDR) method developed by Li et al. (2011), was used to quantify the consistency between pairs of ranked peaks lists from replicates. The IDR methods uses a model that assumes that the ranked lists of peaks in a pair of replicates consist of two groups: a reproducible group and an irreproducible group. In general, the signals in the reproducible group are more consistent (i.e. with a larger rank correlation coefficient) and are ranked higher than the irreproducible group. The proportion of peaks that belong to the irreproducible component and the correlation of the reproducible component are estimated adaptively from the data. The model also provides an IDR score for each peak, which reflects the posterior probability of the peak belonging to the irreproducible group. The aligned reads were pooled from all replicates and the MACS peak caller was used to call significant peaks on the pooled data. Only datasets containing at least 100 peaks passing the IDR threshold were considered valid and submitted for release. As part of the validation of ChIP-seq antibodies and to study the downstream targets of several transcription factors, inducible short hairpin RNA (shRNA) cell lines were generated to knock down the expression of these factors. K562 cells (non-adherent, human erythromyeloblastoid leukemia cell line; ENCODE Tier 1) were transduced with lentiviral vectors carrying an inducible shRNA to a specific transcription factor as described in this protocol. Expression of shRNA was induced with doxycycline in the growth media. Only cell lines that exhibited at least 70% reduction in expression of the targeted transcription factor (determined by qPCR) were used. The cell lines were designated K562-shX, where X is the transcription factor targeted by shRNA and K562 denotes the parent cell line. For example, K562-shATF3 cells are K562 cells selected for stable integration of shRNA targeting the ATF3 gene. Gene expression in doxycycline-induced and uninduced cells were measured and profiled using RNA-seq. The RNA-seq data were submitted to GEO (Accession:GSE33816). Release Notes This is Release 3 (Sept 2012). It contains 110 new experiments including 3 new cell lines and 1 new antibodies. The entire HepG2/HEY1 (Accession: wgEncodeEH001502) and K562/HEY1 (Accession: wgEncodeEH001481) datasets have been revoked due to problems with the quality of the antibody. All experiments with the U87 cell line were remapped. Previously, the sex of the cell was unknown and was mapped to the male genome. It was discovered that the cell line is female. Other files from the previous releases also contained errors. They have been corrected with a version number appended to the name (e.g., V2). shRNA validation data have been included in previous releases. The Verification section above provides a more in-depth explanation of the method. Credits These data were provided by the Myers Lab at the HudsonAlpha Institute for Biotechnology. Contact: Flo Pauli References Fields S. Molecular biology. Site-seeing by sequencing. Science. 2007 Jun 8;316(5830):1441-2. Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007 Jun 8;316(5830):1497-502. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Li Q, Brown JB, Huang H, Bickel PJ. Measuring Reproducibility of High-throughput experiments. Ann. Appl. Stat. Volume 5, Number 3 (2011), 1752-1779. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeTfBindingSuper ENC TF Binding ENCODE Transcription Factor Binding Regulation Description Transcription is regulated through the binding of transcription factor proteins to specific cis-level regulatory sites in the DNA. The nature of this regulation depends on the transcription factor. For example, some proteins activate transcription by recruiting RNA polymerase, some repress transcription by suppressing this recruitment, and others insulate proximal regions from the activity of nearby transcriptional activators or repressors. A key characteristic of each transcription factor protein is its DNA binding domain. Each DNA binding domain recognizes and interacts with DNA that matches a specific nucleotide pattern, or motif. These motifs tend to be short and degenerate, so even when the DNA binding motif is known, one cannot generally predict where a given transcription factor may bind. In general, transcription factor binding is determined experimentally. These tracks contain transcription factor binding sites determined by ChIP-seq. This process involves fragmenting DNA, selecting the fragments of DNA that are bound by a certain transcription factor, and sequencing those DNA fragments. This generally yields a large library of DNA sequences, including some that were bound by the transcription factor directly, some that were bound indirectly via interactions with other molecules, and some false positives (such as cases of nonspecific binding). With the appropriate analysis methods, ChIP-seq can be a valuable approach for elucidating transcription factor binding and cis-level regulation. Display Conventions These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 2007 Jun;17(6):898-909. Hudson ME, Snyder M. High-throughput methods of regulatory element discovery. Biotechniques. 2006 Dec;41(6):673, 675, 677 passim. Data Use Policy External data users may freely download, analyze and publish results based on any ENCODE data without restrictions as soon as they are released. The full policy is available here: ENCODE Data Use Policy for External Users 
wgEncodeHaibTfbsViewRawSignal Raw Signal Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87RxlchV0416101RawRep2V2 U87 RvXL V101 2 RevXlinkChromatin U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-23 2011-05-23 2012-02-23 wgEncodeEH001676 1676 GSM803491 Myers HudsonAlpha SL3777 v041610.1 2 input wgEncodeHaibTfbsU87RxlchV0416101RawRep2V2 None RawSignal glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 Control v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87RxlchV0416101RawRep1V2 U87 RvXL V101 1 RevXlinkChromatin U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-23 2011-05-23 2012-02-23 wgEncodeEH001676 1676 GSM803491 Myers HudsonAlpha SL2338 v041610.1 1 input wgEncodeHaibTfbsU87RxlchV0416101RawRep1V2 None RawSignal glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87RxlchPcr2xRawRep2V2 U87 RvXL PCR2 2 RevXlinkChromatin U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-24 2011-01-21 2011-10-20 wgEncodeEH001559 1559 GSM803375 Myers HudsonAlpha SL414 PCR2x 2 input wgEncodeHaibTfbsU87RxlchPcr2xRawRep2V2 None RawSignal glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 Control PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87RxlchPcr2xRawRep1V2 U87 RvXL PCR2 1 RevXlinkChromatin U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-24 2011-03-08 2011-12-08 wgEncodeEH001559 1559 GSM803375 Myers HudsonAlpha SL103 PCR2x 1 input wgEncodeHaibTfbsU87RxlchPcr2xRawRep1V2 None RawSignal glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87Pol24h8V0416101RawRep2V2 U87 Pol2-4H8 V101 2 Pol2-4H8 U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-23 2011-05-20 2012-02-20 wgEncodeEH001674 1674 GSM803459 Myers HudsonAlpha SL3773 v041610.1 2 exp wgEncodeHaibTfbsU87Pol24h8V0416101RawRep2V2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87Pol24h8V0416101RawRep1V2 U87 Pol2-4H8 V101 1 Pol2-4H8 U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-23 2011-05-20 2012-02-23 wgEncodeEH001674 1674 GSM803459 Myers HudsonAlpha SL1962 v041610.1 1 exp wgEncodeHaibTfbsU87Pol24h8V0416101RawRep1V2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87NrsfPcr2xRawRep2V2 U87 NRSF PCR2 2 NRSF U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-24 2011-01-21 2011-10-20 wgEncodeEH001554 1554 GSM803372 Myers HudsonAlpha SL413 PCR2x 2 exp wgEncodeHaibTfbsU87NrsfPcr2xRawRep2V2 None RawSignal Neuron-restrictive silencer transcription factor glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 NRSF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87NrsfPcr2xRawRep1V2 U87 NRSF PCR2 1 NRSF U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-24 2011-03-08 2011-12-08 wgEncodeEH001554 1554 GSM803372 Myers HudsonAlpha SL88 PCR2x 1 exp wgEncodeHaibTfbsU87NrsfPcr2xRawRep1V2 None RawSignal Neuron-restrictive silencer transcription factor glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) U87 NRSF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dRxlchV0422111RawRep1 T47D RvXL V11 1 RevXlinkChromatin T-47D ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003431 3431 GSM1010884 Myers HudsonAlpha SL13294 v042211.1 1 input wgEncodeHaibTfbsT47dRxlchV0422111RawRep1 None RawSignal epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dRxlchV0416102Dm002p1hRawRep1 T47D RvXL DMSO 1 RevXlinkChromatin T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001631 1631 GSM803433 Myers HudsonAlpha SL1881 v041610.2 1 input wgEncodeHaibTfbsT47dRxlchV0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D Control DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dP300V0416102Dm002p1hRawRep2 T47D p300 DMSO 2 p300 T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001602 1602 GSM803522 Myers HudsonAlpha SL3015 v041610.2 2 exp wgEncodeHaibTfbsT47dP300V0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal EP300(c-20) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D p300 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dP300V0416102Dm002p1hRawRep1 T47D p300 DMSO 1 p300 T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001602 1602 GSM803522 Myers HudsonAlpha SL2633 v041610.2 1 exp wgEncodeHaibTfbsT47dP300V0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal EP300(c-20) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D p300 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dJundV0422111RawRep2 T47D JunD V11 2 JunD T-47D ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003321 3321 GSM1010718 Myers HudsonAlpha SL11657 v042211.1 2 exp wgEncodeHaibTfbsT47dJundV0422111RawRep2 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D JunD v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dJundV0422111RawRep1 T47D JunD V11 1 JunD T-47D ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003321 3321 GSM1010718 Myers HudsonAlpha SL11656 v042211.1 1 exp wgEncodeHaibTfbsT47dJundV0422111RawRep1 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D JunD v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hRawRep2 T47D GATA3 DMSO 2 GATA3_(SC-268) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001639 1639 GSM803514 Myers HudsonAlpha SL3013 v041610.2 2 exp wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D GATA3 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hRawRep1 T47D GATA3 DMSO 1 GATA3_(SC-268) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001639 1639 GSM803514 Myers HudsonAlpha SL2636 v041610.2 1 exp wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D GATA3 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hRawRep2 T47D FOXA1 DMSO 2 FOXA1_(SC-6553) T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001588 1588 GSM803409 Myers HudsonAlpha SL2081 v041610.2 2 exp wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D FOXA1 6553 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hRawRep1 T47D FOXA1 DMSO 1 FOXA1_(SC-6553) T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001588 1588 GSM803409 Myers HudsonAlpha SL1878 v041610.2 1 exp wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D FOXA1 6553 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Gen1hRawRep2 T47 ERa Gen 102 2 ERalpha_a T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001556 1556 GSM803374 Myers HudsonAlpha SL1492 v041610.2 2 exp wgEncodeHaibTfbsT47dEralphaaV0416102Gen1hRawRep2 Genistein_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a Genistein v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Gen1hRawRep1 T47 ERa Gen 102 1 ERalpha_a T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001556 1556 GSM803374 Myers HudsonAlpha SL1218 v041610.2 1 exp wgEncodeHaibTfbsT47dEralphaaV0416102Gen1hRawRep1 Genistein_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a Genistein v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hRawRep2 T47D ERa Estra 2 ERalpha_a T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001577 1577 GSM803539 Myers HudsonAlpha SL1491 v041610.2 2 exp wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hRawRep2 Estradiol_10nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a Estradiol v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hRawRep1 T47D ERa Estra 1 ERalpha_a T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001577 1577 GSM803539 Myers HudsonAlpha SL1217 v041610.2 1 exp wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hRawRep1 Estradiol_10nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a Estradiol v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Dm002p1hRawRep2 T47D ERa DMSO 2 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001601 1601 GSM803519 Myers HudsonAlpha SL1490 v041610.2 2 input wgEncodeHaibTfbsT47dEralphaaV0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Dm002p1hRawRep1 T47D ERa DMSO 1 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001601 1601 GSM803519 Myers HudsonAlpha SL1216 v041610.2 1 input wgEncodeHaibTfbsT47dEralphaaV0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEraaV0416102Bpa1hRawRep2 T47D ERa BPA 2 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002299 2299 GSM1010823 Myers HudsonAlpha SL1877 v041610.2 2 exp wgEncodeHaibTfbsT47dEraaV0416102Bpa1hRawRep2 BPA_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a BPA v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEraaV0416102Bpa1hRawRep1 T47D ERa BPA 1 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002299 2299 GSM1010823 Myers HudsonAlpha SL1493 v041610.2 1 exp wgEncodeHaibTfbsT47dEraaV0416102Bpa1hRawRep1 BPA_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D ERa a BPA v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hRawRep2 T47D CTCF DMSO 2 CTCF_(SC-5916) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001656 1656 GSM803348 Myers HudsonAlpha SL3014 v041610.2 2 exp wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D CTCF 5916 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hRawRep1 T47D CTCF DMSO 1 CTCF_(SC-5916) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001656 1656 GSM803348 Myers HudsonAlpha SL2634 v041610.2 1 exp wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) T-47D CTCF 5916 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraRxlchV0416102RawRep1 SKRA RvXL V102 1 RevXlinkChromatin SK-N-SH_RA ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001606 1606 GSM803526 Myers HudsonAlpha SL2905 v041610.2 1 input wgEncodeHaibTfbsSknshraRxlchV0416102RawRep1 None RawSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA Control v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraYy1sc281V0416102RawRep2 SKRA YY1 V102 2 YY1_(SC-281) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001615 1615 GSM803498 Myers HudsonAlpha SL3640 v041610.2 2 exp wgEncodeHaibTfbsSknshraYy1sc281V0416102RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA YY1 281 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraYy1sc281V0416102RawRep1 SKRA YY1 V102 1 YY1_(SC-281) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001615 1615 GSM803498 Myers HudsonAlpha SL3639 v041610.2 1 exp wgEncodeHaibTfbsSknshraYy1sc281V0416102RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA YY1 281 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraUsf1sc8983V0416102RawRep2 SKRA USF1 V102 2 USF1_(SC-8983) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001621 1621 GSM803472 Myers HudsonAlpha SL2919 v041610.2 2 exp wgEncodeHaibTfbsSknshraUsf1sc8983V0416102RawRep2 None RawSignal This gene encodes a member of the basic helix-loop-helix leucine zipper family, and can function as a cellular transcription factor. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs. This gene has been linked to familial combined hyperlipidemia (FCHL). Two transcript variants encoding distinct isoforms have been identified for this gene. (provided by RefSeq). neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA USF-1 8983 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraUsf1sc8983V0416102RawRep1 SKRA USF1 V102 1 USF1_(SC-8983) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001621 1621 GSM803472 Myers HudsonAlpha SL2911 v041610.2 1 exp wgEncodeHaibTfbsSknshraUsf1sc8983V0416102RawRep1 None RawSignal This gene encodes a member of the basic helix-loop-helix leucine zipper family, and can function as a cellular transcription factor. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs. This gene has been linked to familial combined hyperlipidemia (FCHL). Two transcript variants encoding distinct isoforms have been identified for this gene. (provided by RefSeq). neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA USF-1 8983 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraRad21V0416102RawRep2 SKRA RAD21 V102 2 Rad21 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001614 1614 GSM803497 Myers HudsonAlpha SL2915 v041610.2 2 exp wgEncodeHaibTfbsSknshraRad21V0416102RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA RAD21 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraRad21V0416102RawRep1 SKRA RAD21 V102 1 Rad21 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001614 1614 GSM803497 Myers HudsonAlpha SL2907 v041610.2 1 exp wgEncodeHaibTfbsSknshraRad21V0416102RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA RAD21 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraP300V0416102RawRep2 SKRA p300 V102 2 p300 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001616 1616 GSM803495 Myers HudsonAlpha SL2918 v041610.2 2 exp wgEncodeHaibTfbsSknshraP300V0416102RawRep2 None RawSignal EP300(c-20) neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA p300 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraP300V0416102RawRep1 SKRA p300 V102 1 p300 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001616 1616 GSM803495 Myers HudsonAlpha SL2910 v041610.2 1 exp wgEncodeHaibTfbsSknshraP300V0416102RawRep1 None RawSignal EP300(c-20) neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA p300 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraCtcfV0416102RawRep2 SKRA CTCF V102 2 CTCF SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001613 1613 GSM803333 Myers HudsonAlpha SL2914 v041610.2 2 exp wgEncodeHaibTfbsSknshraCtcfV0416102RawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA CTCF v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraCtcfV0416102RawRep1 SKRA CTCF V102 1 CTCF SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001613 1613 GSM803333 Myers HudsonAlpha SL2906 v041610.2 1 exp wgEncodeHaibTfbsSknshraCtcfV0416102RawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RA CTCF v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcRxlchV0416101RawRep1 SKMC RvXL V101 1 RevXlinkChromatin SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001535 1535 GSM803423 Myers HudsonAlpha SL1714 v041610.1 1 input wgEncodeHaibTfbsSknmcRxlchV0416101RawRep1 None RawSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcRxlchPcr2xRawRep1 SKMC RvXL PCR2 1 RevXlinkChromatin SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-06-02 2012-03-02 wgEncodeEH001677 1677 GSM803492 Myers HudsonAlpha SL102 PCR2x 1 input wgEncodeHaibTfbsSknmcRxlchPcr2xRawRep1 None RawSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcPol24h8V0416101RawRep2 SKMC Pol2-4H8 V101 2 Pol2-4H8 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002281 2281 GSM1010793 Myers HudsonAlpha SL5611 v041610.1 2 exp wgEncodeHaibTfbsSknmcPol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcPol24h8V0416101RawRep1 SKMC Pol2-4H8 V101 1 Pol2-4H8 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002281 2281 GSM1010793 Myers HudsonAlpha SL1963 v041610.1 1 exp wgEncodeHaibTfbsSknmcPol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcFoxp2Pcr2xRawRep2 SKMC FOXP2 PCR2 2 FOXP2 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2008-10-31 2009-07-31 wgEncodeEH001461 1461 GSM803353 Myers HudsonAlpha SL167 PCR2x 2 exp wgEncodeHaibTfbsSknmcFoxp2Pcr2xRawRep2 None RawSignal This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC FOXP2 PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcFoxp2Pcr2xRawRep1 SKMC FOXP2 PCR2 1 FOXP2 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001461 1461 GSM803353 Myers HudsonAlpha SL144 PCR2x 1 exp wgEncodeHaibTfbsSknmcFoxp2Pcr2xRawRep1 None RawSignal This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC FOXP2 PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1RxlchV0416101RawRep1 PFSK RvXL V101 1 RevXlinkChromatin PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002286 2286 GSM1010797 Myers HudsonAlpha SL2339 v041610.1 1 input wgEncodeHaibTfbsPfsk1RxlchV0416101RawRep1 None RawSignal neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1RxlchPcr2xRawRep3 PFSK RvXL PCR2 3 RevXlinkChromatin PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001558 1558 GSM803376 Myers HudsonAlpha SL16 PCR2x 3 input wgEncodeHaibTfbsPfsk1RxlchPcr2xRawRep3 None RawSignal neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Control PCR2x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1RxlchPcr2xRawRep2 PFSK RvXL PCR2 2 RevXlinkChromatin PFSK-1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001558 1558 GSM803376 Myers HudsonAlpha SL412 PCR2x 2 input wgEncodeHaibTfbsPfsk1RxlchPcr2xRawRep2 None RawSignal neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Control PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1RxlchPcr2xRawRep1 PFSK RvXL PCR2 1 RevXlinkChromatin PFSK-1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001558 1558 GSM803376 Myers HudsonAlpha SL150 PCR2x 1 input wgEncodeHaibTfbsPfsk1RxlchPcr2xRawRep1 None RawSignal neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Taf1V0416101RawRep2 PFSK TAF1 V101 2 TAF1 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002309 2309 GSM1010770 Myers HudsonAlpha SL6969 v041610.1 2 exp wgEncodeHaibTfbsPfsk1Taf1V0416101RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 TAF1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Taf1V0416101RawRep1 PFSK TAF1 V101 1 TAF1 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002309 2309 GSM1010770 Myers HudsonAlpha SL3772 v041610.1 1 exp wgEncodeHaibTfbsPfsk1Taf1V0416101RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 TAF1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Sin3ak20V0416101RawRep2 PFSK Sin3A V101 2 Sin3Ak-20 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002268 2268 GSM1010781 Myers HudsonAlpha SL5041 v041610.1 2 exp wgEncodeHaibTfbsPfsk1Sin3ak20V0416101RawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Sin3ak20V0416101RawRep1 PFSK Sin3A V101 1 Sin3Ak-20 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002268 2268 GSM1010781 Myers HudsonAlpha SL2354 v041610.1 1 exp wgEncodeHaibTfbsPfsk1Sin3ak20V0416101RawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Pol24h8V0416101RawRep2 PFSK Pol2-4H8 V101 2 Pol2-4H8 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH002272 2272 GSM1010819 Myers HudsonAlpha SL5610 v041610.1 2 exp wgEncodeHaibTfbsPfsk1Pol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Pol24h8V0416101RawRep1 PFSK Pol2-4H8 V101 1 Pol2-4H8 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH002272 2272 GSM1010819 Myers HudsonAlpha SL2353 v041610.1 1 exp wgEncodeHaibTfbsPfsk1Pol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfV0416101RawRep2 PFSK NRSF V101 2 NRSF PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002267 2267 GSM1010786 Myers HudsonAlpha SL5497 v041610.1 2 exp wgEncodeHaibTfbsPfsk1NrsfV0416101RawRep2 None RawSignal Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 NRSF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfV0416101RawRep1 PFSK NRSF V101 1 NRSF PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002267 2267 GSM1010786 Myers HudsonAlpha SL5496 v041610.1 1 exp wgEncodeHaibTfbsPfsk1NrsfV0416101RawRep1 None RawSignal Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 NRSF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfPcr2xRawRep2 PFSK NRSF PCR2 2 NRSF PFSK-1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001553 1553 GSM803369 Myers HudsonAlpha SL411 PCR2x 2 exp wgEncodeHaibTfbsPfsk1NrsfPcr2xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 NRSF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfPcr2xRawRep1 PFSK NRSF PCR2 1 NRSF PFSK-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001553 1553 GSM803369 Myers HudsonAlpha SL149 PCR2x 1 exp wgEncodeHaibTfbsPfsk1NrsfPcr2xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 NRSF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Foxp2Pcr2xRawRep2 PFSK FOXP2 PCR2 2 FOXP2 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2008-10-31 2009-07-31 wgEncodeEH001460 1460 GSM803480 Myers HudsonAlpha SL14 PCR2x 2 exp wgEncodeHaibTfbsPfsk1Foxp2Pcr2xRawRep2 None RawSignal This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 FOXP2 PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Foxp2Pcr2xRawRep1 PFSK FOXP2 PCR2 1 FOXP2 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001460 1460 GSM803480 Myers HudsonAlpha SL13 PCR2x 1 exp wgEncodeHaibTfbsPfsk1Foxp2Pcr2xRawRep1 None RawSignal This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PFSK-1 FOXP2 PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1RxlchV0422111RawRep1 PANC RvXL V11 1 RevXlinkChromatin PANC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003429 3429 GSM1010853 Myers HudsonAlpha SL16762 v042211.1 1 input wgEncodeHaibTfbsPanc1RxlchV0422111RawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1RxlchV0416101RawRep2 PANC RvXL V101 2 RevXlinkChromatin PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002285 2285 GSM1010796 Myers HudsonAlpha SL3776 v041610.1 2 input wgEncodeHaibTfbsPanc1RxlchV0416101RawRep2 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Control v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1RxlchV0416101RawRep1 PANC RvXL V101 1 RevXlinkChromatin PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002285 2285 GSM1010796 Myers HudsonAlpha SL2340 v041610.1 1 input wgEncodeHaibTfbsPanc1RxlchV0416101RawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1RxlchPcr2xRawRep2 PANC RvXL PCR2 2 RevXlinkChromatin PANC-1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001525 1525 GSM803394 Myers HudsonAlpha SL523 PCR2x 2 input wgEncodeHaibTfbsPanc1RxlchPcr2xRawRep2 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Control PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1RxlchPcr2xRawRep1 PANC RvXL PCR2 1 RevXlinkChromatin PANC-1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001525 1525 GSM803394 Myers HudsonAlpha SL117 PCR2x 1 input wgEncodeHaibTfbsPanc1RxlchPcr2xRawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Sin3ak20V0416101RawRep2 PANC Sin3A V101 2 Sin3Ak-20 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002266 2266 GSM1010785 Myers HudsonAlpha SL5042 v041610.1 2 exp wgEncodeHaibTfbsPanc1Sin3ak20V0416101RawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Sin3ak20V0416101RawRep1 PANC Sin3A V101 1 Sin3Ak-20 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002266 2266 GSM1010785 Myers HudsonAlpha SL2344 v041610.1 1 exp wgEncodeHaibTfbsPanc1Sin3ak20V0416101RawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Pol24h8V0416101RawRep2 PANC Pol2-4H8 V101 2 Pol2-4H8 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002265 2265 GSM1010788 Myers HudsonAlpha SL5609 v041610.1 2 exp wgEncodeHaibTfbsPanc1Pol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Pol24h8V0416101RawRep1 PANC Pol2-4H8 V101 1 Pol2-4H8 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002265 2265 GSM1010788 Myers HudsonAlpha SL2343 v041610.1 1 exp wgEncodeHaibTfbsPanc1Pol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0422111RawRep2 PANC NRSF V11 2 NRSF PANC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003285 3285 GSM1010859 Myers HudsonAlpha SL16342 v042211.1 2 exp wgEncodeHaibTfbsPanc1NrsfV0422111RawRep2 None RawSignal Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 NRSF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0422111RawRep1 PANC NRSF V11 1 NRSF PANC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003285 3285 GSM1010859 Myers HudsonAlpha SL14681 v042211.1 1 exp wgEncodeHaibTfbsPanc1NrsfV0422111RawRep1 None RawSignal Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 NRSF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0416101RawRep2 PANC NRSF V101 2 NRSF PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002280 2280 GSM1010792 Myers HudsonAlpha SL5495 v041610.1 2 exp wgEncodeHaibTfbsPanc1NrsfV0416101RawRep2 None RawSignal Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 NRSF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0416101RawRep1 PANC NRSF V101 1 NRSF PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002280 2280 GSM1010792 Myers HudsonAlpha SL4437 v041610.1 1 exp wgEncodeHaibTfbsPanc1NrsfV0416101RawRep1 None RawSignal Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 NRSF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfPcr2xRawRep2 PANC NRSF PCR2 2 NRSF PANC-1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001552 1552 GSM803370 Myers HudsonAlpha SL522 PCR2x 2 exp wgEncodeHaibTfbsPanc1NrsfPcr2xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 NRSF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfPcr2xRawRep1 PANC NRSF PCR2 1 NRSF PANC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001552 1552 GSM803370 Myers HudsonAlpha SL116 PCR2x 1 exp wgEncodeHaibTfbsPanc1NrsfPcr2xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 NRSF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60RxlchV0422111RawRep2 HL-60 RvXL V11 2 RevXlinkChromatin HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003427 3427 GSM1010870 Myers HudsonAlpha SL16759 v042211.1 2 input wgEncodeHaibTfbsHl60RxlchV0422111RawRep2 None RawSignal promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60RxlchV0422111RawRep1 HL-60 RvXL V11 1 RevXlinkChromatin HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003427 3427 GSM1010870 Myers HudsonAlpha SL12792 v042211.1 1 input wgEncodeHaibTfbsHl60RxlchV0422111RawRep1 None RawSignal promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pu1V0422111RawRep2 HL-60 PU.1 V11 2 PU.1 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003292 3292 GSM1010843 Myers HudsonAlpha SL14712 v042211.1 2 exp wgEncodeHaibTfbsHl60Pu1V0422111RawRep2 None RawSignal PU.1 (H-135) promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 PU.1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pu1V0422111RawRep1 HL-60 PU.1 V11 1 PU.1 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003292 3292 GSM1010843 Myers HudsonAlpha SL12629 v042211.1 1 exp wgEncodeHaibTfbsHl60Pu1V0422111RawRep1 None RawSignal PU.1 (H-135) promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 PU.1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pol24h8V0422111RawRep2 HL-60 Pol2-4H8 V11 2 Pol2-4H8 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003253 3253 GSM1010737 Myers HudsonAlpha SL16322 v042211.1 2 exp wgEncodeHaibTfbsHl60Pol24h8V0422111RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 Pol2-4H8 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pol24h8V0422111RawRep1 HL-60 Pol2-4H8 V11 1 Pol2-4H8 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003253 3253 GSM1010737 Myers HudsonAlpha SL12628 v042211.1 1 exp wgEncodeHaibTfbsHl60Pol24h8V0422111RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 Pol2-4H8 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60NrsfV0422111RawRep2 HL-60 NRSF V11 2 NRSF HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003247 3247 GSM1010754 Myers HudsonAlpha SL13747 v042211.1 2 exp wgEncodeHaibTfbsHl60NrsfV0422111RawRep2 None RawSignal Neuron-restrictive silencer transcription factor promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 NRSF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60NrsfV0422111RawRep1 HL-60 NRSF V11 1 NRSF HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003247 3247 GSM1010754 Myers HudsonAlpha SL12632 v042211.1 1 exp wgEncodeHaibTfbsHl60NrsfV0422111RawRep1 None RawSignal Neuron-restrictive silencer transcription factor promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 NRSF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60GabpV0422111RawRep2 HL-60 GABP V11 2 GABP HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003252 3252 GSM1010822 Myers HudsonAlpha SL16321 v042211.1 2 exp wgEncodeHaibTfbsHl60GabpV0422111RawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 GABP v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60GabpV0422111RawRep1 HL-60 GABP V11 1 GABP HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003252 3252 GSM1010822 Myers HudsonAlpha SL12633 v042211.1 1 exp wgEncodeHaibTfbsHl60GabpV0422111RawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 GABP v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116RxlchV0422111RawRep2 HCT RvXL V11 2 RevXlinkChromatin HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003426 3426 GSM1010872 Myers HudsonAlpha SL12247 v042211.1 2 input wgEncodeHaibTfbsHct116RxlchV0422111RawRep2 None RawSignal colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116RxlchV0422111RawRep1 HCT RvXL V11 1 RevXlinkChromatin HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003426 3426 GSM1010872 Myers HudsonAlpha SL12246 v042211.1 1 input wgEncodeHaibTfbsHct116RxlchV0422111RawRep1 None RawSignal colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116RxlchV0416101RawRep1 HCT RvXL V101 1 RevXlinkChromatin HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001626 1626 GSM803475 Myers HudsonAlpha SL3457 v041610.1 1 input wgEncodeHaibTfbsHct116RxlchV0416101RawRep1 None RawSignal colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Zbtb33V0416101RawRep2 HCT ZBTB33 2 ZBTB33 HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001672 1672 GSM803458 Myers HudsonAlpha SL3970 v041610.1 2 exp wgEncodeHaibTfbsHct116Zbtb33V0416101RawRep2 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 ZBTB33 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Zbtb33V0416101RawRep1 HCT ZBTB33 1 ZBTB33 HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001672 1672 GSM803458 Myers HudsonAlpha SL3646 v041610.1 1 exp wgEncodeHaibTfbsHct116Zbtb33V0416101RawRep1 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 ZBTB33 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Yy1sc281V0416101RawRep2 HCT YY1 V101 2 YY1_(SC-281) HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001671 1671 GSM803354 Myers HudsonAlpha SL4500 v041610.1 2 exp wgEncodeHaibTfbsHct116Yy1sc281V0416101RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Yy1sc281V0416101RawRep1 HCT YY1 V101 1 YY1_(SC-281) HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001671 1671 GSM803354 Myers HudsonAlpha SL3971 v041610.1 1 exp wgEncodeHaibTfbsHct116Yy1sc281V0416101RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Usf1V0422111RawRep2 HCT USF1 V11 2 USF-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003310 3310 GSM1010836 Myers HudsonAlpha SL16733 v042211.1 2 exp wgEncodeHaibTfbsHct116Usf1V0422111RawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 USF-1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Usf1V0422111RawRep1 HCT USF1 V11 1 USF-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003310 3310 GSM1010836 Myers HudsonAlpha SL12238 v042211.1 1 exp wgEncodeHaibTfbsHct116Usf1V0422111RawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 USF-1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Tead4sc101184V0422111RawRep2 HCT TEAD4 V11 2 TEAD4_(SC-101184) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003309 3309 GSM1010772 Myers HudsonAlpha SL14570 v042211.1 2 exp wgEncodeHaibTfbsHct116Tead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Tead4sc101184V0422111RawRep1 HCT TEAD4 V11 1 TEAD4_(SC-101184) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003309 3309 GSM1010772 Myers HudsonAlpha SL16313 v042211.1 1 exp wgEncodeHaibTfbsHct116Tead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116SrfV0422111RawRep2 HCT SRF V11 2 SRF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003218 3218 GSM1010851 Myers HudsonAlpha SL13070 v042211.1 2 exp wgEncodeHaibTfbsHct116SrfV0422111RawRep2 None RawSignal Serum response transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 SRF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116SrfV0422111RawRep1 HCT SRF V11 1 SRF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003218 3218 GSM1010851 Myers HudsonAlpha SL12237 v042211.1 1 exp wgEncodeHaibTfbsHct116SrfV0422111RawRep1 None RawSignal Serum response transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 SRF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sp1V0422111RawRep2 HCT SP1 V11 2 SP1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003221 3221 GSM1010902 Myers HudsonAlpha SL13072 v042211.1 2 exp wgEncodeHaibTfbsHct116Sp1V0422111RawRep2 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 SP1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sp1V0422111RawRep1 HCT SP1 V11 1 SP1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003221 3221 GSM1010902 Myers HudsonAlpha SL12239 v042211.1 1 exp wgEncodeHaibTfbsHct116Sp1V0422111RawRep1 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 SP1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sin3ak20V0422111RawRep2 HCT Sin3A V11 2 Sin3Ak-20 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003222 3222 GSM1010905 Myers HudsonAlpha SL13076 v042211.1 2 exp wgEncodeHaibTfbsHct116Sin3ak20V0422111RawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Sin3Ak-20 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sin3ak20V0422111RawRep1 HCT Sin3A V11 1 Sin3Ak-20 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003222 3222 GSM1010905 Myers HudsonAlpha SL12244 v042211.1 1 exp wgEncodeHaibTfbsHct116Sin3ak20V0422111RawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Sin3Ak-20 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Rad21V0422111RawRep2 HCT RAD21 V11 2 Rad21 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003217 3217 GSM1010848 Myers HudsonAlpha SL13067 v042211.1 2 exp wgEncodeHaibTfbsHct116Rad21V0422111RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 RAD21 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Rad21V0422111RawRep1 HCT RAD21 V11 1 Rad21 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003217 3217 GSM1010848 Myers HudsonAlpha SL12230 v042211.1 1 exp wgEncodeHaibTfbsHct116Rad21V0422111RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 RAD21 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Pol24h8V0416101RawRep2 HCT Pol2-4H8 V101 2 Pol2-4H8 HCT-116 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001627 1627 GSM803474 Myers HudsonAlpha SL3830 v041610.1 2 exp wgEncodeHaibTfbsHct116Pol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Pol24h8V0416101RawRep1 HCT Pol2-4H8 V101 1 Pol2-4H8 HCT-116 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001627 1627 GSM803474 Myers HudsonAlpha SL3456 v041610.1 1 exp wgEncodeHaibTfbsHct116Pol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116NrsfV0422111RawRep2 HCT NRSF V11 2 NRSF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003308 3308 GSM1010869 Myers HudsonAlpha SL14560 v042211.1 2 exp wgEncodeHaibTfbsHct116NrsfV0422111RawRep2 None RawSignal Neuron-restrictive silencer transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 NRSF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116NrsfV0422111RawRep1 HCT NRSF V11 1 NRSF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003308 3308 GSM1010869 Myers HudsonAlpha SL16310 v042211.1 1 exp wgEncodeHaibTfbsHct116NrsfV0422111RawRep1 None RawSignal Neuron-restrictive silencer transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 NRSF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116MaxV0422111RawRep2 HCT Max V11 2 Max HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003223 3223 GSM1010904 Myers HudsonAlpha SL13075 v042211.1 2 exp wgEncodeHaibTfbsHct116MaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116MaxV0422111RawRep1 HCT Max V11 1 Max HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003223 3223 GSM1010904 Myers HudsonAlpha SL12243 v042211.1 1 exp wgEncodeHaibTfbsHct116MaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116JundV0422111RawRep2 HCT JunD V11 2 JunD HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003216 3216 GSM1010847 Myers HudsonAlpha SL13069 v042211.1 2 exp wgEncodeHaibTfbsHct116JundV0422111RawRep2 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 JunD v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116JundV0422111RawRep1 HCT JunD V11 1 JunD HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003216 3216 GSM1010847 Myers HudsonAlpha SL12233 v042211.1 1 exp wgEncodeHaibTfbsHct116JundV0422111RawRep1 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 JunD v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Fosl1V0422111RawRep2 HCT FOSL1 V11 2 FOSL1_(SC-183) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003246 3246 GSM1010756 Myers HudsonAlpha SL13068 v042211.1 2 exp wgEncodeHaibTfbsHct116Fosl1V0422111RawRep2 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 FOSL1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Fosl1V0422111RawRep1 HCT FOSL1 V11 1 FOSL1_(SC-183) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003246 3246 GSM1010756 Myers HudsonAlpha SL12231 v042211.1 1 exp wgEncodeHaibTfbsHct116Fosl1V0422111RawRep1 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 FOSL1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Elf1V0422111RawRep2 HCT ELF1 V11 2 ELF1_(SC-631) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003307 3307 GSM1010765 Myers HudsonAlpha SL13733 v042211.1 2 exp wgEncodeHaibTfbsHct116Elf1V0422111RawRep2 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 ELF1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Elf1V0422111RawRep1 HCT ELF1 V11 1 ELF1_(SC-631) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003307 3307 GSM1010765 Myers HudsonAlpha SL14719 v042211.1 1 exp wgEncodeHaibTfbsHct116Elf1V0422111RawRep1 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 ELF1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Egr1V0422111RawRep2 HCT Egr-1 V11 2 Egr-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003215 3215 GSM1010846 Myers HudsonAlpha SL13065 v042211.1 2 exp wgEncodeHaibTfbsHct116Egr1V0422111RawRep2 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Egr-1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Egr1V0422111RawRep1 HCT Egr-1 V11 1 Egr-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003215 3215 GSM1010846 Myers HudsonAlpha SL12228 v042211.1 1 exp wgEncodeHaibTfbsHct116Egr1V0422111RawRep1 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Egr-1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116CtcfcV0422111RawRep2 HCT CTCF V11 2 CTCF_(SC-5916) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003220 3220 GSM1010903 Myers HudsonAlpha SL13074 v042211.1 2 exp wgEncodeHaibTfbsHct116CtcfcV0422111RawRep2 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CTCF 5916 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116CtcfcV0422111RawRep1 HCT CTCF V11 1 CTCF_(SC-5916) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003220 3220 GSM1010903 Myers HudsonAlpha SL12242 v042211.1 1 exp wgEncodeHaibTfbsHct116CtcfcV0422111RawRep1 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CTCF 5916 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cebpbsc150V0422111RawRep2 HCT CEBPB V11 2 CEBPB_(SC-150) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003219 3219 GSM1010852 Myers HudsonAlpha SL13073 v042211.1 2 exp wgEncodeHaibTfbsHct116Cebpbsc150V0422111RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CEBPB v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cebpbsc150V0422111RawRep1 HCT CEBPB V11 1 CEBPB_(SC-150) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003219 3219 GSM1010852 Myers HudsonAlpha SL12240 v042211.1 1 exp wgEncodeHaibTfbsHct116Cebpbsc150V0422111RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CEBPB v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cbx3sc101004V0422111RawRep2 HCT CBX3 V11 2 CBX3_(SC-101004) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003277 3277 GSM1010758 Myers HudsonAlpha SL13066 v042211.1 2 exp wgEncodeHaibTfbsHct116Cbx3sc101004V0422111RawRep2 None RawSignal At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CBX3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cbx3sc101004V0422111RawRep1 HCT CBX3 V11 1 CBX3_(SC-101004) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003277 3277 GSM1010758 Myers HudsonAlpha SL12229 v042211.1 1 exp wgEncodeHaibTfbsHct116Cbx3sc101004V0422111RawRep1 None RawSignal At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CBX3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Atf3V0422111RawRep2 HCT ATF3 V11 2 ATF3 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003276 3276 GSM1010757 Myers HudsonAlpha SL16874 v042211.1 2 exp wgEncodeHaibTfbsHct116Atf3V0422111RawRep2 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 ATF3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Atf3V0422111RawRep1 HCT ATF3 V11 1 ATF3 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003276 3276 GSM1010757 Myers HudsonAlpha SL12234 v042211.1 1 exp wgEncodeHaibTfbsHct116Atf3V0422111RawRep1 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 ATF3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892RxlchV0416102RawRep1 GM92 RvXL V102 1 RevXlinkChromatin GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001510 1510 GSM803488 Myers HudsonAlpha SL818 v041610.2 1 input wgEncodeHaibTfbsGm12892RxlchV0416102RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 Control v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892RxlchV0416101RawRep1 GM92 RvXL V101 1 RevXlinkChromatin GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001518 1518 GSM803482 Myers HudsonAlpha SL1783 v041610.1 1 input wgEncodeHaibTfbsGm12892RxlchV0416101RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Yy1V0416101RawRep2 GM92 YY1 V101 2 YY1 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001609 1609 GSM803516 Myers HudsonAlpha SL3584 v041610.1 2 exp wgEncodeHaibTfbsGm12892Yy1V0416101RawRep2 None RawSignal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 YY1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Yy1V0416101RawRep1 GM92 YY1 V101 1 YY1 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001609 1609 GSM803516 Myers HudsonAlpha SL2132 v041610.1 1 exp wgEncodeHaibTfbsGm12892Yy1V0416101RawRep1 None RawSignal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 YY1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Taf1V0416102RawRep2 GM92 TAF1 V102 2 TAF1 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001513 1513 GSM803489 Myers HudsonAlpha SL945 v041610.2 2 exp wgEncodeHaibTfbsGm12892Taf1V0416102RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 TAF1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Taf1V0416102RawRep1 GM92 TAF1 V102 1 TAF1 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001513 1513 GSM803489 Myers HudsonAlpha SL736 v041610.2 1 exp wgEncodeHaibTfbsGm12892Taf1V0416102RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 TAF1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep2 GM92 Pol2-4H8 V102 2 Pol2-4H8 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001512 1512 GSM803490 Myers HudsonAlpha SL946 v041610.2 2 exp wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 Pol2-4H8 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep1 GM92 Pol2-4H8 V102 1 Pol2-4H8 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001512 1512 GSM803490 Myers HudsonAlpha SL911 v041610.2 1 exp wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 Pol2-4H8 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol2V0416102RawRep2 GM92 Pol2 V102 2 Pol2 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001511 1511 GSM803487 Myers HudsonAlpha SL944 v041610.2 2 exp wgEncodeHaibTfbsGm12892Pol2V0416102RawRep2 None RawSignal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 Pol2 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol2V0416102RawRep1 GM92 Pol2 V102 1 Pol2 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001511 1511 GSM803487 Myers HudsonAlpha SL909 v041610.2 1 exp wgEncodeHaibTfbsGm12892Pol2V0416102RawRep1 None RawSignal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 Pol2 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pax5c20V0416101RawRep2 GM92 PAX5 V101 2 PAX5-C20 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001546 1546 GSM803334 Myers HudsonAlpha SL2133 v041610.1 2 exp wgEncodeHaibTfbsGm12892Pax5c20V0416101RawRep2 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 PAX5-C20 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pax5c20V0416101RawRep1 GM92 PAX5 V101 1 PAX5-C20 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001546 1546 GSM803334 Myers HudsonAlpha SL1664 v041610.1 1 exp wgEncodeHaibTfbsGm12892Pax5c20V0416101RawRep1 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12892 PAX5-C20 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891RxlchV0416101RawRep1 GM91 RvXL V101 1 RevXlinkChromatin GM12891 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001592 1592 GSM803467 Myers HudsonAlpha SL1782 v041610.1 1 input wgEncodeHaibTfbsGm12891RxlchV0416101RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891RxlchPcr1xRawRep1 GM91 RvXL PCR1 1 RevXlinkChromatin GM12891 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001519 1519 GSM803481 Myers HudsonAlpha SL817 PCR1x 1 input wgEncodeHaibTfbsGm12891RxlchPcr1xRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Yy1sc281V0416101RawRep2 GM91 YY1 V101 2 YY1_(SC-281) GM12891 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001573 1573 GSM803535 Myers HudsonAlpha SL2130 v041610.1 2 exp wgEncodeHaibTfbsGm12891Yy1sc281V0416101RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Yy1sc281V0416101RawRep1 GM91 YY1 V101 1 YY1_(SC-281) GM12891 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001573 1573 GSM803535 Myers HudsonAlpha SL2388 v041610.1 1 exp wgEncodeHaibTfbsGm12891Yy1sc281V0416101RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Taf1Pcr1xRawRep2 GM91 TAF1 PCR1 2 TAF1 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001524 1524 GSM803393 Myers HudsonAlpha SL920 PCR1x 2 exp wgEncodeHaibTfbsGm12891Taf1Pcr1xRawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 TAF1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Taf1Pcr1xRawRep1 GM91 TAF1 PCR1 1 TAF1 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001524 1524 GSM803393 Myers HudsonAlpha SL749 PCR1x 1 exp wgEncodeHaibTfbsGm12891Taf1Pcr1xRawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 TAF1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pu1Pcr1xRawRep2 GM91 PU.1 PCR1 2 PU.1 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001521 1521 GSM803398 Myers HudsonAlpha SL948 PCR1x 2 exp wgEncodeHaibTfbsGm12891Pu1Pcr1xRawRep2 None RawSignal PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 PU.1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pu1Pcr1xRawRep1 GM91 PU.1 PCR1 1 PU.1 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001521 1521 GSM803398 Myers HudsonAlpha SL977 PCR1x 1 exp wgEncodeHaibTfbsGm12891Pu1Pcr1xRawRep1 None RawSignal PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 PU.1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pou2f2Pcr1xRawRep2 GM91 POU2F2 2 POU2F2 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001520 1520 GSM803397 Myers HudsonAlpha SL918 PCR1x 2 exp wgEncodeHaibTfbsGm12891Pou2f2Pcr1xRawRep2 None RawSignal Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 POU2F2 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pou2f2Pcr1xRawRep1 GM91 POU2F2 1 POU2F2 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001520 1520 GSM803397 Myers HudsonAlpha SL802 PCR1x 1 exp wgEncodeHaibTfbsGm12891Pou2f2Pcr1xRawRep1 None RawSignal Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 POU2F2 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol24h8Pcr1xRawRep2 GM91 Pol2-4H8 PCR1 2 Pol2-4H8 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001523 1523 GSM803400 Myers HudsonAlpha SL922 PCR1x 2 exp wgEncodeHaibTfbsGm12891Pol24h8Pcr1xRawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 Pol2-4H8 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol24h8Pcr1xRawRep1 GM91 Pol2-4H8 PCR1 1 Pol2-4H8 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001523 1523 GSM803400 Myers HudsonAlpha SL910 PCR1x 1 exp wgEncodeHaibTfbsGm12891Pol24h8Pcr1xRawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 Pol2-4H8 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol2Pcr1xRawRep2 GM91 Pol2 PCR1 2 Pol2 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001522 1522 GSM803399 Myers HudsonAlpha SL921 PCR1x 2 exp wgEncodeHaibTfbsGm12891Pol2Pcr1xRawRep2 None RawSignal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 Pol2 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol2Pcr1xRawRep1 GM91 Pol2 PCR1 1 Pol2 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001522 1522 GSM803399 Myers HudsonAlpha SL908 PCR1x 1 exp wgEncodeHaibTfbsGm12891Pol2Pcr1xRawRep1 None RawSignal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 Pol2 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pax5c20V0416101RawRep2 GM91 PAX5 V101 2 PAX5-C20 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001545 1545 GSM803337 Myers HudsonAlpha SL2131 v041610.1 2 exp wgEncodeHaibTfbsGm12891Pax5c20V0416101RawRep2 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 PAX5-C20 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pax5c20V0416101RawRep1 GM91 PAX5 V101 1 PAX5-C20 GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001545 1545 GSM803337 Myers HudsonAlpha SL1662 v041610.1 1 exp wgEncodeHaibTfbsGm12891Pax5c20V0416101RawRep1 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12891 PAX5-C20 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1RxlchV0422111RawRep2 ECC1 RvXL V11 2 RevXlinkChromatin ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003424 3424 GSM1010874 Myers HudsonAlpha SL16754 v042211.1 2 input wgEncodeHaibTfbsEcc1RxlchV0422111RawRep2 None RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1RxlchV0422111RawRep1 ECC1 RvXL V11 1 RevXlinkChromatin ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003424 3424 GSM1010874 Myers HudsonAlpha SL13506 v042211.1 1 input wgEncodeHaibTfbsEcc1RxlchV0422111RawRep1 None RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1RxlchV0416102Dm002p1hRawRep1 ECC1 RvXL DMSO 1 RevXlinkChromatin ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001587 1587 GSM803445 Myers HudsonAlpha SL1882 v041610.2 1 input wgEncodeHaibTfbsEcc1RxlchV0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Control DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Zbtb7aV0422111RawRep2 ECC1 ZBTB7A 2 ZBTB7A_(SC-34508) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003241 3241 GSM1010752 Myers HudsonAlpha SL14586 v042211.1 2 exp wgEncodeHaibTfbsEcc1Zbtb7aV0422111RawRep2 None RawSignal Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ZBTB7A v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Zbtb7aV0422111RawRep1 ECC1 ZBTB7A 1 ZBTB7A_(SC-34508) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003241 3241 GSM1010752 Myers HudsonAlpha SL13275 v042211.1 1 exp wgEncodeHaibTfbsEcc1Zbtb7aV0422111RawRep1 None RawSignal Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ZBTB7A v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Yy1sc281V0422111RawRep2 ECC1 YY1 V11 2 YY1_(SC-281) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003240 3240 GSM1010753 Myers HudsonAlpha SL14584 v042211.1 2 exp wgEncodeHaibTfbsEcc1Yy1sc281V0422111RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 YY1 281 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Yy1sc281V0422111RawRep1 ECC1 YY1 V11 1 YY1_(SC-281) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003240 3240 GSM1010753 Myers HudsonAlpha SL13273 v042211.1 1 exp wgEncodeHaibTfbsEcc1Yy1sc281V0422111RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 YY1 281 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Usf1V0422111RawRep2 ECC1 USF1 V11 2 USF-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003239 3239 GSM1010886 Myers HudsonAlpha SL14589 v042211.1 2 exp wgEncodeHaibTfbsEcc1Usf1V0422111RawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 USF-1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Usf1V0422111RawRep1 ECC1 USF1 V11 1 USF-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003239 3239 GSM1010886 Myers HudsonAlpha SL13279 v042211.1 1 exp wgEncodeHaibTfbsEcc1Usf1V0422111RawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 USF-1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tead4sc101184V0422111RawRep2 ECC1 TEAD4 V11 2 TEAD4_(SC-101184) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003238 3238 GSM1010885 Myers HudsonAlpha SL14591 v042211.1 2 exp wgEncodeHaibTfbsEcc1Tead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tead4sc101184V0422111RawRep1 ECC1 TEAD4 V11 1 TEAD4_(SC-101184) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003238 3238 GSM1010885 Myers HudsonAlpha SL13281 v042211.1 1 exp wgEncodeHaibTfbsEcc1Tead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tcf12V0422111RawRep2 ECC1 TCF12 V11 2 TCF12 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003291 3291 GSM1010842 Myers HudsonAlpha SL14063 v042211.1 2 exp wgEncodeHaibTfbsEcc1Tcf12V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 TCF12 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tcf12V0422111RawRep1 ECC1 TCF12 V11 1 TCF12 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003291 3291 GSM1010842 Myers HudsonAlpha SL16025 v042211.1 1 exp wgEncodeHaibTfbsEcc1Tcf12V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 TCF12 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Taf1V0422111RawRep2 ECC1 TAF1 V11 2 TAF1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003256 3256 GSM1010733 Myers HudsonAlpha SL14721 v042211.1 2 exp wgEncodeHaibTfbsEcc1Taf1V0422111RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 TAF1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Taf1V0422111RawRep1 ECC1 TAF1 V11 1 TAF1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003256 3256 GSM1010733 Myers HudsonAlpha SL13751 v042211.1 1 exp wgEncodeHaibTfbsEcc1Taf1V0422111RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 TAF1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1SrfV0422111RawRep2 ECC1 SRF V11 2 SRF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003245 3245 GSM1010762 Myers HudsonAlpha SL14583 v042211.1 2 exp wgEncodeHaibTfbsEcc1SrfV0422111RawRep2 None RawSignal Serum response transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 SRF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1SrfV0422111RawRep1 ECC1 SRF V11 1 SRF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003245 3245 GSM1010762 Myers HudsonAlpha SL13272 v042211.1 1 exp wgEncodeHaibTfbsEcc1SrfV0422111RawRep1 None RawSignal Serum response transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 SRF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Rad21V0422111RawRep2 ECC1 RAD21 V11 2 Rad21 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003263 3263 GSM1010801 Myers HudsonAlpha SL16305 v042211.1 2 exp wgEncodeHaibTfbsEcc1Rad21V0422111RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 RAD21 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Rad21V0422111RawRep1 ECC1 RAD21 V11 1 Rad21 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003263 3263 GSM1010801 Myers HudsonAlpha SL13270 v042211.1 1 exp wgEncodeHaibTfbsEcc1Rad21V0422111RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 RAD21 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hRawRep2 ECC1 Pol2 DMSO 2 Pol2 ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001572 1572 GSM803536 Myers HudsonAlpha SL2085 v041610.2 2 exp wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal RNA Polymerase II epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Pol2 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hRawRep1 ECC1 Pol2 DMSO 1 Pol2 ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001572 1572 GSM803536 Myers HudsonAlpha SL1176 v041610.2 1 exp wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal RNA Polymerase II epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Pol2 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1P300V0422111RawRep2 ECC1 p300 V11 2 p300 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003274 3274 GSM1010759 Myers HudsonAlpha SL14585 v042211.1 2 exp wgEncodeHaibTfbsEcc1P300V0422111RawRep2 None RawSignal EP300(c-20) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 p300 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1P300V0422111RawRep1 ECC1 p300 V11 1 p300 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003274 3274 GSM1010759 Myers HudsonAlpha SL13274 v042211.1 1 exp wgEncodeHaibTfbsEcc1P300V0422111RawRep1 None RawSignal EP300(c-20) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 p300 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1NrsfV0422111RawRep2 ECC1 NRSF V11 2 NRSF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003290 3290 GSM1010841 Myers HudsonAlpha SL14057 v042211.1 2 exp wgEncodeHaibTfbsEcc1NrsfV0422111RawRep2 None RawSignal Neuron-restrictive silencer transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 NRSF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1NrsfV0422111RawRep1 ECC1 NRSF V11 1 NRSF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003290 3290 GSM1010841 Myers HudsonAlpha SL16023 v042211.1 1 exp wgEncodeHaibTfbsEcc1NrsfV0422111RawRep1 None RawSignal Neuron-restrictive silencer transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 NRSF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Nficsc81335V0422111RawRep2 ECC1 NFIC V11 2 NFIC_(SC-81335) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003289 3289 GSM1010855 Myers HudsonAlpha SL16022 v042211.1 2 exp wgEncodeHaibTfbsEcc1Nficsc81335V0422111RawRep2 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 NFIC v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Nficsc81335V0422111RawRep1 ECC1 NFIC V11 1 NFIC_(SC-81335) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003289 3289 GSM1010855 Myers HudsonAlpha SL14056 v042211.1 1 exp wgEncodeHaibTfbsEcc1Nficsc81335V0422111RawRep1 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 NFIC v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1MaxV0422111RawRep2 ECC1 Max V11 2 Max ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003268 3268 GSM1010807 Myers HudsonAlpha SL16021 v042211.1 2 exp wgEncodeHaibTfbsEcc1MaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1MaxV0422111RawRep1 ECC1 Max V11 1 Max ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003268 3268 GSM1010807 Myers HudsonAlpha SL14054 v042211.1 1 exp wgEncodeHaibTfbsEcc1MaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1GrV0416102Etoh02RawRep2 ECC1 GR EtOH 2 GR ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001591 1591 GSM803464 Myers HudsonAlpha SL1087 v041610.2 2 input wgEncodeHaibTfbsEcc1GrV0416102Etoh02RawRep2 EtOH_0.02pct RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 GR EtOH v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1GrV0416102Etoh02RawRep1 ECC1 GR EtOH 1 GR ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001591 1591 GSM803464 Myers HudsonAlpha SL1035 v041610.2 1 input wgEncodeHaibTfbsEcc1GrV0416102Etoh02RawRep1 EtOH_0.02pct RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 GR EtOH v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1GrV0416102Dex100nmRawRep2 ECC1 GR DEX 102 2 GR ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001540 1540 GSM803340 Myers HudsonAlpha SL1088 v041610.2 2 exp wgEncodeHaibTfbsEcc1GrV0416102Dex100nmRawRep2 DEX_100nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 GR DEX 100nM v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1GrV0416102Dex100nmRawRep1 ECC1 GR DEX 102 1 GR ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001540 1540 GSM803340 Myers HudsonAlpha SL1012 v041610.2 1 exp wgEncodeHaibTfbsEcc1GrV0416102Dex100nmRawRep1 DEX_100nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 GR DEX 100nM v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxm1sc502V0422111RawRep2 ECC1 FOXM1 V11 2 FOXM1_(SC-502) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003288 3288 GSM1010856 Myers HudsonAlpha SL14725 v042211.1 2 exp wgEncodeHaibTfbsEcc1Foxm1sc502V0422111RawRep2 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 FOXM1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxm1sc502V0422111RawRep1 ECC1 FOXM1 V11 1 FOXM1_(SC-502) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003288 3288 GSM1010856 Myers HudsonAlpha SL14051 v042211.1 1 exp wgEncodeHaibTfbsEcc1Foxm1sc502V0422111RawRep1 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 FOXM1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hRawRep2 ECC1 FOXA1 DMSO 2 FOXA1_(SC-6553) ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001586 1586 GSM803444 Myers HudsonAlpha SL2080 v041610.2 2 exp wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 FOXA1 6553 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hRawRep1 ECC1 FOXA1 DMSO 1 FOXA1_(SC-6553) ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001586 1586 GSM803444 Myers HudsonAlpha SL1880 v041610.2 1 exp wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 FOXA1 6553 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hRawRep2 ECC1 ERa Geni 2 ERalpha_a ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001575 1575 GSM803541 Myers HudsonAlpha SL1122 v041610.2 2 exp wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hRawRep2 Genistein_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a Genistein v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hRawRep1 ECC1 ERa Geni 1 ERalpha_a ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001575 1575 GSM803541 Myers HudsonAlpha SL1049 v041610.2 1 exp wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hRawRep1 Genistein_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a Genistein v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hRawRep2 ECC1 ERa Estra 2 ERalpha_a ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001536 1536 GSM803422 Myers HudsonAlpha SL1093 v041610.2 2 exp wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hRawRep2 Estradiol_10nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a Estradiol v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hRawRep1 ECC1 ERa Estra 1 ERalpha_a ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001536 1536 GSM803422 Myers HudsonAlpha SL1011 v041610.2 1 exp wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hRawRep1 Estradiol_10nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a Estradiol v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Dm002p1hRawRep2 ECC1 ERa DMSO 2 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001537 1537 GSM803421 Myers HudsonAlpha SL1092 v041610.2 2 input wgEncodeHaibTfbsEcc1EralphaaV0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Dm002p1hRawRep1 ECC1 ERa DMSO 1 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001537 1537 GSM803421 Myers HudsonAlpha SL1034 v041610.2 1 input wgEncodeHaibTfbsEcc1EralphaaV0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hRawRep2 ECC1 ERa BPA 2 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002313 2313 GSM1010747 Myers HudsonAlpha SL2082 v041610.2 2 exp wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hRawRep2 BPA_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a BPA v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hRawRep1 ECC1 ERa BPA 1 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002313 2313 GSM1010747 Myers HudsonAlpha SL1050 v041610.2 1 exp wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hRawRep1 BPA_100nM RawSignal This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 ERa a BPA v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Egr1V0422111RawRep2 ECC1 Egr-1 V11 2 Egr-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003232 3232 GSM1010888 Myers HudsonAlpha SL14590 v042211.1 2 exp wgEncodeHaibTfbsEcc1Egr1V0422111RawRep2 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Egr-1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Egr1V0422111RawRep1 ECC1 Egr-1 V11 1 Egr-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003232 3232 GSM1010888 Myers HudsonAlpha SL13280 v042211.1 1 exp wgEncodeHaibTfbsEcc1Egr1V0422111RawRep1 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 Egr-1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hRawRep2 ECC1 CTCF DMSO 2 CTCF_(SC-5916) ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002300 2300 GSM1010774 Myers HudsonAlpha SL3447 v041610.2 2 exp wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hRawRep2 DMSO_0.02pct RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 CTCF 5916 DMSO v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hRawRep1 ECC1 CTCF DMSO 1 CTCF_(SC-5916) ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002300 2300 GSM1010774 Myers HudsonAlpha SL2630 v041610.2 1 exp wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hRawRep1 DMSO_0.02pct RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 CTCF 5916 DMSO v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Creb1sc240V0422111RawRep2 ECC1 CREB1 V11 2 CREB1_(SC-240) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003287 3287 GSM1010857 Myers HudsonAlpha SL14723 v042211.1 2 exp wgEncodeHaibTfbsEcc1Creb1sc240V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 CREB1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Creb1sc240V0422111RawRep1 ECC1 CREB1 V11 1 CREB1_(SC-240) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003287 3287 GSM1010857 Myers HudsonAlpha SL14048 v042211.1 1 exp wgEncodeHaibTfbsEcc1Creb1sc240V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 CREB1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Cebpbsc150V0422111RawRep2 ECC1 CEBPB V11 2 CEBPB_(SC-150) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003262 3262 GSM1010802 Myers HudsonAlpha SL16302 v042211.1 2 exp wgEncodeHaibTfbsEcc1Cebpbsc150V0422111RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 CEBPB v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Cebpbsc150V0422111RawRep1 ECC1 CEBPB V11 1 CEBPB_(SC-150) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003262 3262 GSM1010802 Myers HudsonAlpha SL13276 v042211.1 1 exp wgEncodeHaibTfbsEcc1Cebpbsc150V0422111RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) ECC-1 CEBPB v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0422111RawRep4 SKSH RvXL V11 4 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003430 3430 GSM1010883 Myers HudsonAlpha SL16761 v042211.1 4 input wgEncodeHaibTfbsSknshRxlchV0422111RawRep4 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v042211.1 ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0422111RawRep3 SKSH RvXL V11 3 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003430 3430 GSM1010883 Myers HudsonAlpha SL13505 v042211.1 3 input wgEncodeHaibTfbsSknshRxlchV0422111RawRep3 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v042211.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0422111RawRep2 SKSH RvXL V11 2 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003430 3430 GSM1010883 Myers HudsonAlpha SL16760 v042211.1 2 input wgEncodeHaibTfbsSknshRxlchV0422111RawRep2 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0422111RawRep1 SKSH RvXL V11 1 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003430 3430 GSM1010883 Myers HudsonAlpha SL12791 v042211.1 1 input wgEncodeHaibTfbsSknshRxlchV0422111RawRep1 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0416101RawRep3 SKSH RvXL V101 3 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002287 2287 GSM1010798 Myers HudsonAlpha SL3775 v041610.1 3 input wgEncodeHaibTfbsSknshRxlchV0416101RawRep3 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v041610.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0416101RawRep2 SKSH RvXL V101 2 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002287 2287 GSM1010798 Myers HudsonAlpha SL3774 v041610.1 2 input wgEncodeHaibTfbsSknshRxlchV0416101RawRep2 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchV0416101RawRep1 SKSH RvXL V101 1 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002287 2287 GSM1010798 Myers HudsonAlpha SL2134 v041610.1 1 input wgEncodeHaibTfbsSknshRxlchV0416101RawRep1 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchPcr2xRawRep2 SKSH RvXL PCR2 2 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001473 1473 GSM803528 Myers HudsonAlpha SL410 PCR2x 2 input wgEncodeHaibTfbsSknshRxlchPcr2xRawRep2 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxlchPcr2xRawRep1 SKSH RvXL PCR2 1 RevXlinkChromatin SK-N-SH ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001473 1473 GSM803528 Myers HudsonAlpha SL108 PCR2x 1 input wgEncodeHaibTfbsSknshRxlchPcr2xRawRep1 None RawSignal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshZbtb33V0422111RawRep2 SKSH ZBTB33 V11 2 ZBTB33 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003261 3261 GSM1010799 Myers HudsonAlpha SL14711 v042211.1 2 exp wgEncodeHaibTfbsSknshZbtb33V0422111RawRep2 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH ZBTB33 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshZbtb33V0422111RawRep1 SKSH ZBTB33 V11 1 ZBTB33 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003261 3261 GSM1010799 Myers HudsonAlpha SL13502 v042211.1 1 exp wgEncodeHaibTfbsSknshZbtb33V0422111RawRep1 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH ZBTB33 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshYy1sc281V0422111RawRep2 SKSH YY1 V11 2 YY1_(SC-281) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003228 3228 GSM1010897 Myers HudsonAlpha SL14045 v042211.1 2 exp wgEncodeHaibTfbsSknshYy1sc281V0422111RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH YY1 281 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshYy1sc281V0422111RawRep1 SKSH YY1 V11 1 YY1_(SC-281) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003228 3228 GSM1010897 Myers HudsonAlpha SL13085 v042211.1 1 exp wgEncodeHaibTfbsSknshYy1sc281V0422111RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH YY1 281 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshUsf1V0422111RawRep2 SKSH USF1 V11 2 USF-1 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003269 3269 GSM1010806 Myers HudsonAlpha SL14597 v042211.1 2 exp wgEncodeHaibTfbsSknshUsf1V0422111RawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH USF-1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshUsf1V0422111RawRep1 SKSH USF1 V11 1 USF-1 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003269 3269 GSM1010806 Myers HudsonAlpha SL13084 v042211.1 1 exp wgEncodeHaibTfbsSknshUsf1V0422111RawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH USF-1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTead4sc101184V0422111RawRep2 SKSH TEAD4 V11 2 TEAD4_(SC-101184) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003286 3286 GSM1010858 Myers HudsonAlpha SL14710 v042211.1 2 exp wgEncodeHaibTfbsSknshTead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTead4sc101184V0422111RawRep1 SKSH TEAD4 V11 1 TEAD4_(SC-101184) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003286 3286 GSM1010858 Myers HudsonAlpha SL13501 v042211.1 1 exp wgEncodeHaibTfbsSknshTead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTcf12V0422111RawRep2 SKSH TCF12 V11 2 TCF12 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003227 3227 GSM1010900 Myers HudsonAlpha SL14046 v042211.1 2 exp wgEncodeHaibTfbsSknshTcf12V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH TCF12 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTcf12V0422111RawRep1 SKSH TCF12 V11 1 TCF12 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003227 3227 GSM1010900 Myers HudsonAlpha SL13086 v042211.1 1 exp wgEncodeHaibTfbsSknshTcf12V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH TCF12 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTaf1V0416101RawRep2 SKSH TAF1 V101 2 TAF1 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002301 2301 GSM1010773 Myers HudsonAlpha SL6462 v041610.1 2 exp wgEncodeHaibTfbsSknshTaf1V0416101RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH TAF1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTaf1V0416101RawRep1 SKSH TAF1 V101 1 TAF1 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002301 2301 GSM1010773 Myers HudsonAlpha SL5612 v041610.1 1 exp wgEncodeHaibTfbsSknshTaf1V0416101RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH TAF1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshSin3ak20V0416101RawRep2 SKSH Sin3A V101 2 Sin3Ak-20 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002271 2271 GSM1010816 Myers HudsonAlpha SL5895 v041610.1 2 exp wgEncodeHaibTfbsSknshSin3ak20V0416101RawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshSin3ak20V0416101RawRep1 SKSH Sin3A V101 1 Sin3Ak-20 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002271 2271 GSM1010816 Myers HudsonAlpha SL5043 v041610.1 1 exp wgEncodeHaibTfbsSknshSin3ak20V0416101RawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxraV0422111RawRep2 SKSH RXRA V11 2 RXRA SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003302 3302 GSM1010767 Myers HudsonAlpha SL14708 v042211.1 2 exp wgEncodeHaibTfbsSknshRxraV0422111RawRep2 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RXRA v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxraV0422111RawRep1 SKSH RXRA V11 1 RXRA SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003302 3302 GSM1010767 Myers HudsonAlpha SL13497 v042211.1 1 exp wgEncodeHaibTfbsSknshRxraV0422111RawRep1 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH RXRA v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPol24h8V0416101RawRep2 SKSH Pol2-4H8 V101 2 Pol2-4H8 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002270 2270 GSM1010817 Myers HudsonAlpha SL5607 v041610.1 2 exp wgEncodeHaibTfbsSknshPol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPol24h8V0416101RawRep1 SKSH Pol2-4H8 V101 1 Pol2-4H8 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002270 2270 GSM1010817 Myers HudsonAlpha SL3768 v041610.1 1 exp wgEncodeHaibTfbsSknshPol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPbx3V0422111RawRep2 SKSH PBx3 V11 2 Pbx3 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003300 3300 GSM1010887 Myers HudsonAlpha SL16042 v042211.1 2 exp wgEncodeHaibTfbsSknshPbx3V0422111RawRep2 None RawSignal Pbx 3 (D-17) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH PBx3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPbx3V0422111RawRep1 SKSH PBx3 V11 1 Pbx3 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003300 3300 GSM1010887 Myers HudsonAlpha SL13495 v042211.1 1 exp wgEncodeHaibTfbsSknshPbx3V0422111RawRep1 None RawSignal Pbx 3 (D-17) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH PBx3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshP300V0422111RawRep2 SKSH p300 V11 2 p300 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003270 3270 GSM1010763 Myers HudsonAlpha SL14705 v042211.1 2 exp wgEncodeHaibTfbsSknshP300V0422111RawRep2 None RawSignal EP300(c-20) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH p300 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshP300V0422111RawRep1 SKSH p300 V11 1 p300 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003270 3270 GSM1010763 Myers HudsonAlpha SL13494 v042211.1 1 exp wgEncodeHaibTfbsSknshP300V0422111RawRep1 None RawSignal EP300(c-20) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH p300 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfV0416101RawRep2 SKSH NRSF V101 2 NRSF SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002269 2269 GSM1010735 Myers HudsonAlpha SL5896 v041610.1 2 exp wgEncodeHaibTfbsSknshNrsfV0416101RawRep2 None RawSignal Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH NRSF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfV0416101RawRep1 SKSH NRSF V101 1 NRSF SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002269 2269 GSM1010735 Myers HudsonAlpha SL5494 v041610.1 1 exp wgEncodeHaibTfbsSknshNrsfV0416101RawRep1 None RawSignal Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH NRSF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfPcr2xRawRep2 SKSH NRSF PCR2 2 NRSF SK-N-SH ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001547 1547 GSM803335 Myers HudsonAlpha SL409 PCR2x 2 exp wgEncodeHaibTfbsSknshNrsfPcr2xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH NRSF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfPcr2xRawRep1 SKSH NRSF PCR2 1 NRSF SK-N-SH ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001547 1547 GSM803335 Myers HudsonAlpha SL83 PCR2x 1 exp wgEncodeHaibTfbsSknshNrsfPcr2xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH NRSF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNficsc81335V0422111RawRep2 SKSH NFIC V11 2 NFIC_(SC-81335) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-18 wgEncodeEH003237 3237 GSM1010880 Myers HudsonAlpha SL14603 v042211.1 2 exp wgEncodeHaibTfbsSknshNficsc81335V0422111RawRep2 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH NFIC v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNficsc81335V0422111RawRep1 SKSH NFIC V11 1 NFIC_(SC-81335) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-18 wgEncodeEH003237 3237 GSM1010880 Myers HudsonAlpha SL13313 v042211.1 1 exp wgEncodeHaibTfbsSknshNficsc81335V0422111RawRep1 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH NFIC v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMef2aV0422111RawRep2 SKSH MEF2A V11 2 MEF2A SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003298 3298 GSM1010834 Myers HudsonAlpha SL14704 v042211.1 2 exp wgEncodeHaibTfbsSknshMef2aV0422111RawRep2 None RawSignal The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH MEF2A v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMef2aV0422111RawRep1 SKSH MEF2A V11 1 MEF2A SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003298 3298 GSM1010834 Myers HudsonAlpha SL13493 v042211.1 1 exp wgEncodeHaibTfbsSknshMef2aV0422111RawRep1 None RawSignal The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH MEF2A v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMaxV0422111RawRep2 SKSH Max V11 2 Max SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003299 3299 GSM1010835 Myers HudsonAlpha SL16738 v042211.1 2 exp wgEncodeHaibTfbsSknshMaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMaxV0422111RawRep1 SKSH Max V11 1 Max SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003299 3299 GSM1010835 Myers HudsonAlpha SL14602 v042211.1 1 exp wgEncodeHaibTfbsSknshMaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshJundV0422111RawRep2 SKSH JunD V11 2 JunD SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003226 3226 GSM1010901 Myers HudsonAlpha SL14042 v042211.1 2 exp wgEncodeHaibTfbsSknshJundV0422111RawRep2 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH JunD v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshJundV0422111RawRep1 SKSH JunD V11 1 JunD SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003226 3226 GSM1010901 Myers HudsonAlpha SL13079 v042211.1 1 exp wgEncodeHaibTfbsSknshJundV0422111RawRep1 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH JunD v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGata3V0422111RawRep2 SKSH GATA3 V11 2 GATA3_(SC-268) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003249 3249 GSM1010738 Myers HudsonAlpha SL14041 v042211.1 2 exp wgEncodeHaibTfbsSknshGata3V0422111RawRep2 None RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH GATA3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGata3V0422111RawRep1 SKSH GATA3 V11 1 GATA3_(SC-268) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003249 3249 GSM1010738 Myers HudsonAlpha SL13078 v042211.1 1 exp wgEncodeHaibTfbsSknshGata3V0422111RawRep1 None RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH GATA3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGabpV0422111RawRep2 SKSH GABP V11 2 GABP SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003248 3248 GSM1010739 Myers HudsonAlpha SL13752 v042211.1 2 exp wgEncodeHaibTfbsSknshGabpV0422111RawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH GABP v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGabpV0422111RawRep1 SKSH GABP V11 1 GABP SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003248 3248 GSM1010739 Myers HudsonAlpha SL12627 v042211.1 1 exp wgEncodeHaibTfbsSknshGabpV0422111RawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH GABP v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFoxm1sc502V0422111RawRep2 SKSH FOXM1 V11 2 FOXM1_(SC-502) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003243 3243 GSM1010750 Myers HudsonAlpha SL14596 v042211.1 2 exp wgEncodeHaibTfbsSknshFoxm1sc502V0422111RawRep2 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH FOXM1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFoxm1sc502V0422111RawRep1 SKSH FOXM1 V11 1 FOXM1_(SC-502) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003243 3243 GSM1010750 Myers HudsonAlpha SL13083 v042211.1 1 exp wgEncodeHaibTfbsSknshFoxm1sc502V0422111RawRep1 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH FOXM1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFosl2V0422111RawRep2 SKSH FOSL2 V11 2 FOSL2 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003297 3297 GSM1010840 Myers HudsonAlpha SL16737 v042211.1 2 exp wgEncodeHaibTfbsSknshFosl2V0422111RawRep2 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH FOSL2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFosl2V0422111RawRep1 SKSH FOSL2 V11 1 FOSL2 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003297 3297 GSM1010840 Myers HudsonAlpha SL13310 v042211.1 1 exp wgEncodeHaibTfbsSknshFosl2V0422111RawRep1 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH FOSL2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshElf1V0422111RawRep2 SKSH ELF1 V11 2 ELF1_(SC-631) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003242 3242 GSM1010751 Myers HudsonAlpha SL14600 v042211.1 2 exp wgEncodeHaibTfbsSknshElf1V0422111RawRep2 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH ELF1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshElf1V0422111RawRep1 SKSH ELF1 V11 1 ELF1_(SC-631) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003242 3242 GSM1010751 Myers HudsonAlpha SL13309 v042211.1 1 exp wgEncodeHaibTfbsSknshElf1V0422111RawRep1 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH ELF1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7RxlchV0422111RawRep4 MCF-7 RvXL V11 4 RevXlinkChromatin MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003428 3428 GSM1010854 Myers HudsonAlpha SL16758 v042211.1 4 input wgEncodeHaibTfbsMcf7RxlchV0422111RawRep4 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Control v042211.1 ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7RxlchV0422111RawRep3 MCF-7 RvXL V11 3 RevXlinkChromatin MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003428 3428 GSM1010854 Myers HudsonAlpha SL16757 v042211.1 3 input wgEncodeHaibTfbsMcf7RxlchV0422111RawRep3 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Control v042211.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7RxlchV0422111RawRep2 MCF-7 RvXL V11 2 RevXlinkChromatin MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003428 3428 GSM1010854 Myers HudsonAlpha SL16756 v042211.1 2 input wgEncodeHaibTfbsMcf7RxlchV0422111RawRep2 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7RxlchV0422111RawRep1 MCF-7 RvXL V11 1 RevXlinkChromatin MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003428 3428 GSM1010854 Myers HudsonAlpha SL13504 v042211.1 1 input wgEncodeHaibTfbsMcf7RxlchV0422111RawRep1 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tead4sc101184V0422111RawRep2 MCF-7 TEAD4 V11 2 TEAD4_(SC-101184) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003284 3284 GSM1010860 Myers HudsonAlpha SL16341 v042211.1 2 exp wgEncodeHaibTfbsMcf7Tead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tead4sc101184V0422111RawRep1 MCF-7 TEAD4 V11 1 TEAD4_(SC-101184) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003284 3284 GSM1010860 Myers HudsonAlpha SL14575 v042211.1 1 exp wgEncodeHaibTfbsMcf7Tead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tcf12V0422111RawRep2 MCF-7 TCF12 V11 2 TCF12 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003283 3283 GSM1010861 Myers HudsonAlpha SL16340 v042211.1 2 exp wgEncodeHaibTfbsMcf7Tcf12V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 TCF12 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tcf12V0422111RawRep1 MCF-7 TCF12 V11 1 TCF12 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003283 3283 GSM1010861 Myers HudsonAlpha SL14574 v042211.1 1 exp wgEncodeHaibTfbsMcf7Tcf12V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 TCF12 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Taf1V0422111RawRep2 MCF-7 TAF1 V11 2 TAF1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003317 3317 GSM1010811 Myers HudsonAlpha SL16339 v042211.1 2 exp wgEncodeHaibTfbsMcf7Taf1V0422111RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 TAF1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Taf1V0422111RawRep1 MCF-7 TAF1 V11 1 TAF1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003317 3317 GSM1010811 Myers HudsonAlpha SL14572 v042211.1 1 exp wgEncodeHaibTfbsMcf7Taf1V0422111RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 TAF1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7SrfV0422111RawRep2 MCF-7 SRF V11 2 SRF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003296 3296 GSM1010839 Myers HudsonAlpha SL16044 v042211.1 2 exp wgEncodeHaibTfbsMcf7SrfV0422111RawRep2 None RawSignal Serum response transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 SRF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7SrfV0422111RawRep1 MCF-7 SRF V11 1 SRF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003296 3296 GSM1010839 Myers HudsonAlpha SL13723 v042211.1 1 exp wgEncodeHaibTfbsMcf7SrfV0422111RawRep1 None RawSignal Serum response transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 SRF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Sin3ak20V0422111RawRep2 MCF-7 Sin3A V11 2 Sin3Ak-20 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003282 3282 GSM1010862 Myers HudsonAlpha SL14716 v042211.1 2 exp wgEncodeHaibTfbsMcf7Sin3ak20V0422111RawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Sin3Ak-20 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Sin3ak20V0422111RawRep1 MCF-7 Sin3A V11 1 Sin3Ak-20 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003282 3282 GSM1010862 Myers HudsonAlpha SL13726 v042211.1 1 exp wgEncodeHaibTfbsMcf7Sin3ak20V0422111RawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Sin3Ak-20 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Rad21V0422111RawRep2 MCF-7 RAD21 V11 2 Rad21 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003259 3259 GSM1010791 Myers HudsonAlpha SL16336 v042211.1 2 exp wgEncodeHaibTfbsMcf7Rad21V0422111RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 RAD21 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Rad21V0422111RawRep1 MCF-7 RAD21 V11 1 Rad21 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003259 3259 GSM1010791 Myers HudsonAlpha SL13724 v042211.1 1 exp wgEncodeHaibTfbsMcf7Rad21V0422111RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 RAD21 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Pmlsc71910V0422111RawRep2 MCF-7 PML V11 2 PML_(SC-71910) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003295 3295 GSM1010838 Myers HudsonAlpha SL16026 v042211.1 2 exp wgEncodeHaibTfbsMcf7Pmlsc71910V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 PML v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Pmlsc71910V0422111RawRep1 MCF-7 PML V11 1 PML_(SC-71910) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003295 3295 GSM1010838 Myers HudsonAlpha SL13722 v042211.1 1 exp wgEncodeHaibTfbsMcf7Pmlsc71910V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 PML v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7P300V0422111RawRep2 MCF-7 p300 V11 2 p300 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003260 3260 GSM1010800 Myers HudsonAlpha SL16335 v042211.1 2 exp wgEncodeHaibTfbsMcf7P300V0422111RawRep2 None RawSignal EP300(c-20) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 p300 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7P300V0422111RawRep1 MCF-7 p300 V11 1 p300 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003260 3260 GSM1010800 Myers HudsonAlpha SL13492 v042211.1 1 exp wgEncodeHaibTfbsMcf7P300V0422111RawRep1 None RawSignal EP300(c-20) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 p300 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7NrsfV0422111RawRep2 MCF-7 NRSF V11 2 NRSF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003231 3231 GSM1010891 Myers HudsonAlpha SL14698 v042211.1 2 exp wgEncodeHaibTfbsMcf7NrsfV0422111RawRep2 None RawSignal Neuron-restrictive silencer transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 NRSF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7NrsfV0422111RawRep1 MCF-7 NRSF V11 1 NRSF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003231 3231 GSM1010891 Myers HudsonAlpha SL13491 v042211.1 1 exp wgEncodeHaibTfbsMcf7NrsfV0422111RawRep1 None RawSignal Neuron-restrictive silencer transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 NRSF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111RawRep2 MCF-7 NR2F2 V11 2 NR2F2_(SC-271940) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003294 3294 GSM1010837 Myers HudsonAlpha SL14697 v042211.1 2 exp wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111RawRep2 None RawSignal This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 NR2F2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111RawRep1 MCF-7 NR2F2 V11 1 NR2F2_(SC-271940) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003294 3294 GSM1010837 Myers HudsonAlpha SL13490 v042211.1 1 exp wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111RawRep1 None RawSignal This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 NR2F2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7MaxV0422111RawRep2 MCF-7 Max V11 2 Max MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003281 3281 GSM1010863 Myers HudsonAlpha SL14695 v042211.1 2 exp wgEncodeHaibTfbsMcf7MaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7MaxV0422111RawRep1 MCF-7 Max V11 1 Max MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003281 3281 GSM1010863 Myers HudsonAlpha SL13485 v042211.1 1 exp wgEncodeHaibTfbsMcf7MaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7JundV0422111RawRep2 MCF-7 JunD V11 2 JunD MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003236 3236 GSM1010892 Myers HudsonAlpha SL14694 v042211.1 2 exp wgEncodeHaibTfbsMcf7JundV0422111RawRep2 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 JunD v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7JundV0422111RawRep1 MCF-7 JunD V11 1 JunD MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003236 3236 GSM1010892 Myers HudsonAlpha SL13484 v042211.1 1 exp wgEncodeHaibTfbsMcf7JundV0422111RawRep1 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 JunD v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111RawRep2 MCF-7 HDAC2 V11 2 HDAC2_(SC-6296) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003258 3258 GSM1010825 Myers HudsonAlpha SL16334 v042211.1 2 exp wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111RawRep2 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 HDAC2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111RawRep1 MCF-7 HDAC2 V11 1 HDAC2_(SC-6296) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003258 3258 GSM1010825 Myers HudsonAlpha SL13483 v042211.1 1 exp wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111RawRep1 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 HDAC2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Gata3V0422111RawRep2 MCF-7 GATA3 V11 2 GATA3_(SC-268) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003235 3235 GSM1010783 Myers HudsonAlpha SL14692 v042211.1 2 exp wgEncodeHaibTfbsMcf7Gata3V0422111RawRep2 None RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 GATA3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Gata3V0422111RawRep1 MCF-7 GATA3 V11 1 GATA3_(SC-268) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003235 3235 GSM1010783 Myers HudsonAlpha SL13482 v042211.1 1 exp wgEncodeHaibTfbsMcf7Gata3V0422111RawRep1 None RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 GATA3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7GabpV0422111RawRep2 MCF-7 GABP V11 2 GABP MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003280 3280 GSM1010864 Myers HudsonAlpha SL14683 v042211.1 2 exp wgEncodeHaibTfbsMcf7GabpV0422111RawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 GABP v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7GabpV0422111RawRep1 MCF-7 GABP V11 1 GABP MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003280 3280 GSM1010864 Myers HudsonAlpha SL13459 v042211.1 1 exp wgEncodeHaibTfbsMcf7GabpV0422111RawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 GABP v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Foxm1sc502V0422111RawRep2 MCF-7 FOXM1 V11 2 FOXM1_(SC-502) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003279 3279 GSM1010769 Myers HudsonAlpha SL14686 v042211.1 2 exp wgEncodeHaibTfbsMcf7Foxm1sc502V0422111RawRep2 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 FOXM1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Foxm1sc502V0422111RawRep1 MCF-7 FOXM1 V11 1 FOXM1_(SC-502) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003279 3279 GSM1010769 Myers HudsonAlpha SL13462 v042211.1 1 exp wgEncodeHaibTfbsMcf7Foxm1sc502V0422111RawRep1 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 FOXM1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Fosl2V0422111RawRep2 MCF-7 FOSL2 V11 2 FOSL2 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003278 3278 GSM1010768 Myers HudsonAlpha SL14682 v042211.1 2 exp wgEncodeHaibTfbsMcf7Fosl2V0422111RawRep2 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 FOSL2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Fosl2V0422111RawRep1 MCF-7 FOSL2 V11 1 FOSL2 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003278 3278 GSM1010768 Myers HudsonAlpha SL13457 v042211.1 1 exp wgEncodeHaibTfbsMcf7Fosl2V0422111RawRep1 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 FOSL2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Elf1V0422111RawRep2 MCF-7 ELF1 V11 2 ELF1_(SC-631) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003234 3234 GSM1010764 Myers HudsonAlpha SL14690 v042211.1 2 exp wgEncodeHaibTfbsMcf7Elf1V0422111RawRep2 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 ELF1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Elf1V0422111RawRep1 MCF-7 ELF1 V11 1 ELF1_(SC-631) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003234 3234 GSM1010764 Myers HudsonAlpha SL13466 v042211.1 1 exp wgEncodeHaibTfbsMcf7Elf1V0422111RawRep1 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 ELF1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Egr1V0422111RawRep2 MCF-7 Egr-1 V11 2 Egr-1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003293 3293 GSM1010844 Myers HudsonAlpha SL14689 v042211.1 2 exp wgEncodeHaibTfbsMcf7Egr1V0422111RawRep2 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Egr-1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Egr1V0422111RawRep1 MCF-7 Egr-1 V11 1 Egr-1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003293 3293 GSM1010844 Myers HudsonAlpha SL13465 v042211.1 1 exp wgEncodeHaibTfbsMcf7Egr1V0422111RawRep1 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Egr-1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7CtcfcV0422111RawRep2 MCF-7 CTCF V11 2 CTCF_(SC-5916) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003257 3257 GSM1010734 Myers HudsonAlpha SL16333 v042211.1 2 exp wgEncodeHaibTfbsMcf7CtcfcV0422111RawRep2 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 CTCF 5916 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7CtcfcV0422111RawRep1 MCF-7 CTCF V11 1 CTCF_(SC-5916) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003257 3257 GSM1010734 Myers HudsonAlpha SL13463 v042211.1 1 exp wgEncodeHaibTfbsMcf7CtcfcV0422111RawRep1 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 CTCF 5916 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Cebpbsc150V0422111RawRep2 MCF-7 CEBPB V11 2 CEBPB_(SC-150) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003233 3233 GSM1010889 Myers HudsonAlpha SL14684 v042211.1 2 exp wgEncodeHaibTfbsMcf7Cebpbsc150V0422111RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 CEBPB v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Cebpbsc150V0422111RawRep1 MCF-7 CEBPB V11 1 CEBPB_(SC-150) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003233 3233 GSM1010889 Myers HudsonAlpha SL13460 v042211.1 1 exp wgEncodeHaibTfbsMcf7Cebpbsc150V0422111RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 CEBPB v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecRxlchPcr1xRawRep1 HUVEC RvXL PCR1 1 RevXlinkChromatin HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH001675 1675 GSM1010736 Myers HudsonAlpha SL1106 PCR1x 1 input wgEncodeHaibTfbsHuvecRxlchPcr1xRawRep1 None RawSignal umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol24h8V0416101RawRep2 HUVEC Pol2-4H8 V101 2 Pol2-4H8 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002298 2298 GSM1010824 Myers HudsonAlpha SL2387 v041610.1 2 exp wgEncodeHaibTfbsHuvecPol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol24h8V0416101RawRep1 HUVEC Pol2-4H8 V101 1 Pol2-4H8 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002298 2298 GSM1010824 Myers HudsonAlpha SL1104 v041610.1 1 exp wgEncodeHaibTfbsHuvecPol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol2Pcr1xRawRep2 HUVEC Pol2 PCR1 2 Pol2 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002297 2297 GSM1010830 Myers HudsonAlpha SL6966 PCR1x 2 exp wgEncodeHaibTfbsHuvecPol2Pcr1xRawRep2 None RawSignal RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Pol2 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol2Pcr1xRawRep1 HUVEC Pol2 PCR1 1 Pol2 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002297 2297 GSM1010830 Myers HudsonAlpha SL1103 PCR1x 1 exp wgEncodeHaibTfbsHuvecPol2Pcr1xRawRep1 None RawSignal RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Pol2 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchV0422111RawRep3 HepG RvXL V11 3 RevXlinkChromatin HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH002277 2277 GSM1010814 Myers HudsonAlpha SL12795 v042211.1 3 input wgEncodeHaibTfbsHepg2RxlchV0422111RawRep3 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control v042211.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchV0422111RawRep2 HepG RvXL V11 2 RevXlinkChromatin HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH002277 2277 GSM1010814 Myers HudsonAlpha SL12050 v042211.1 2 input wgEncodeHaibTfbsHepg2RxlchV0422111RawRep2 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchV0422111RawRep1 HepG RvXL V11 1 RevXlinkChromatin HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002277 2277 GSM1010814 Myers HudsonAlpha SL6019 v042211.1 1 input wgEncodeHaibTfbsHepg2RxlchV0422111RawRep1 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchV0416101RawRep2 HepG RvXL V101 2 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001596 1596 GSM803463 Myers HudsonAlpha SL3976 v041610.1 2 input wgEncodeHaibTfbsHepg2RxlchV0416101RawRep2 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchV0416101RawRep1 HepG RvXL V101 1 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001596 1596 GSM803463 Myers HudsonAlpha SL1781 v041610.1 1 input wgEncodeHaibTfbsHepg2RxlchV0416101RawRep1 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchPcr2xRawRep2 HepG RvXL PCR2 2 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001597 1597 GSM803462 Myers HudsonAlpha SL295 PCR2x 2 input wgEncodeHaibTfbsHepg2RxlchPcr2xRawRep2 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchPcr2xRawRep1 HepG RvXL PCR2 1 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001597 1597 GSM803462 Myers HudsonAlpha SL294 PCR2x 1 input wgEncodeHaibTfbsHepg2RxlchPcr2xRawRep1 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep4 HepG RvXL PCR1 4 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001603 1603 GSM803521 Myers HudsonAlpha SL1401 PCR1x 4 input wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep4 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control PCR1x ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep3 HepG RvXL PCR1 3 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001603 1603 GSM803521 Myers HudsonAlpha SL1400 PCR1x 3 input wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep3 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control PCR1x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep2 HepG RvXL PCR1 2 RevXlinkChromatin HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001603 1603 GSM803521 Myers HudsonAlpha SL819 PCR1x 2 input wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep2 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep1 HepG RvXL PCR1 1 RevXlinkChromatin HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001603 1603 GSM803521 Myers HudsonAlpha SL593 PCR1x 1 input wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep1 None RawSignal hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zeb1V0422111RawRep2 HepG ZEB1 V11 2 ZEB1_(SC-25388) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003315 3315 GSM1010809 Myers HudsonAlpha SL16318 v042211.1 2 exp wgEncodeHaibTfbsHepg2Zeb1V0422111RawRep2 None RawSignal This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZEB1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zeb1V0422111RawRep1 HepG ZEB1 V11 1 ZEB1_(SC-25388) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003315 3315 GSM1010809 Myers HudsonAlpha SL13301 v042211.1 1 exp wgEncodeHaibTfbsHepg2Zeb1V0422111RawRep1 None RawSignal This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZEB1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb7aV0416101RawRep2 HepG ZBTB7A 2 ZBTB7A_(SC-34508) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002296 2296 GSM1010831 Myers HudsonAlpha SL6464 v041610.1 2 exp wgEncodeHaibTfbsHepg2Zbtb7aV0416101RawRep2 None RawSignal Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZBTB7A v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb7aV0416101RawRep1 HepG ZBTB7A 1 ZBTB7A_(SC-34508) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002296 2296 GSM1010831 Myers HudsonAlpha SL3973 v041610.1 1 exp wgEncodeHaibTfbsHepg2Zbtb7aV0416101RawRep1 None RawSignal Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZBTB7A v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33V0416101RawRep2 HepG ZBTB33 2 ZBTB33 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001642 1642 GSM803418 Myers HudsonAlpha SL3987 v041610.1 2 exp wgEncodeHaibTfbsHepg2Zbtb33V0416101RawRep2 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZBTB33 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33V0416101RawRep1 HepG ZBTB33 1 ZBTB33 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001642 1642 GSM803418 Myers HudsonAlpha SL3929 v041610.1 1 exp wgEncodeHaibTfbsHepg2Zbtb33V0416101RawRep1 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZBTB33 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33Pcr1xRawRep2 HepG ZBTB33 2 ZBTB33 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001503 1503 GSM803449 Myers HudsonAlpha SL1055 PCR1x 2 exp wgEncodeHaibTfbsHepg2Zbtb33Pcr1xRawRep2 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZBTB33 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33Pcr1xRawRep1 HepG ZBTB33 1 ZBTB33 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001503 1503 GSM803449 Myers HudsonAlpha SL981 PCR1x 1 exp wgEncodeHaibTfbsHepg2Zbtb33Pcr1xRawRep1 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ZBTB33 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Yy1sc281V0416101RawRep2 HepG YY1 V101 2 YY1_(SC-281) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001661 1661 GSM803381 Myers HudsonAlpha SL3927 v041610.1 2 exp wgEncodeHaibTfbsHepg2Yy1sc281V0416101RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Yy1sc281V0416101RawRep1 HepG YY1 V101 1 YY1_(SC-281) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001661 1661 GSM803381 Myers HudsonAlpha SL2195 v041610.1 1 exp wgEncodeHaibTfbsHepg2Yy1sc281V0416101RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Usf1Pcr1xRawRep2 HepG USF1 PCR1 2 USF-1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001472 1472 GSM803527 Myers HudsonAlpha SL636 PCR1x 2 exp wgEncodeHaibTfbsHepg2Usf1Pcr1xRawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 USF-1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Usf1Pcr1xRawRep1 HepG USF1 PCR1 1 USF-1 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-21 2011-12-21 wgEncodeEH001472 1472 GSM803527 Myers HudsonAlpha SL582 PCR1x 1 exp wgEncodeHaibTfbsHepg2Usf1Pcr1xRawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 USF-1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tead4sc101184V0422111RawRep2 HepG TEAD4 V11 2 TEAD4_(SC-101184) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002345 2345 GSM1010875 Myers HudsonAlpha SL9545 v042211.1 2 exp wgEncodeHaibTfbsHepg2Tead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tead4sc101184V0422111RawRep1 HepG TEAD4 V11 1 TEAD4_(SC-101184) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002345 2345 GSM1010875 Myers HudsonAlpha SL8584 v042211.1 1 exp wgEncodeHaibTfbsHepg2Tead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tcf12Pcr1xRawRep2 HepG TCF12 PCR1 2 TCF12 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001544 1544 GSM803336 Myers HudsonAlpha SL1167 PCR1x 2 exp wgEncodeHaibTfbsHepg2Tcf12Pcr1xRawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 TCF12 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tcf12Pcr1xRawRep1 HepG TCF12 PCR1 1 TCF12 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001544 1544 GSM803336 Myers HudsonAlpha SL1060 PCR1x 1 exp wgEncodeHaibTfbsHepg2Tcf12Pcr1xRawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 TCF12 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Taf1Pcr2xRawRep2 HepG TAF1 PCR2 2 TAF1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001551 1551 GSM803367 Myers HudsonAlpha SL359 PCR2x 2 exp wgEncodeHaibTfbsHepg2Taf1Pcr2xRawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 TAF1 PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Taf1Pcr2xRawRep1 HepG TAF1 PCR2 1 TAF1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001551 1551 GSM803367 Myers HudsonAlpha SL358 PCR2x 1 exp wgEncodeHaibTfbsHepg2Taf1Pcr2xRawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 TAF1 PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2SrfV0416101RawRep2 HepG SRF V101 2 SRF HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001611 1611 GSM803502 Myers HudsonAlpha SL3275 v041610.1 2 exp wgEncodeHaibTfbsHepg2SrfV0416101RawRep2 None RawSignal Serum response transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 SRF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2SrfV0416101RawRep1 HepG SRF V101 1 SRF HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001611 1611 GSM803502 Myers HudsonAlpha SL3156 v041610.1 1 exp wgEncodeHaibTfbsHepg2SrfV0416101RawRep1 None RawSignal Serum response transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 SRF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp2V0422111RawRep2 HepG SP2 V11 2 SP2_(SC-643) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002264 2264 GSM1010787 Myers HudsonAlpha SL6006 v042211.1 2 exp wgEncodeHaibTfbsHepg2Sp2V0422111RawRep2 None RawSignal This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 SP2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp2V0422111RawRep1 HepG SP2 V11 1 SP2_(SC-643) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002264 2264 GSM1010787 Myers HudsonAlpha SL5688 v042211.1 1 exp wgEncodeHaibTfbsHepg2Sp2V0422111RawRep1 None RawSignal This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 SP2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp1Pcr1xRawRep2 HepG SP1 PCR1 2 SP1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001561 1561 GSM803507 Myers HudsonAlpha SL1194 PCR1x 2 exp wgEncodeHaibTfbsHepg2Sp1Pcr1xRawRep2 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 SP1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp1Pcr1xRawRep1 HepG SP1 PCR1 1 SP1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001561 1561 GSM803507 Myers HudsonAlpha SL1056 PCR1x 1 exp wgEncodeHaibTfbsHepg2Sp1Pcr1xRawRep1 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 SP1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xRawRep2 HepG Sin3A PCR1 2 Sin3Ak-20 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001471 1471 GSM803530 Myers HudsonAlpha SL637 PCR1x 2 exp wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xRawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Sin3Ak-20 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xRawRep1 HepG Sin3A PCR1 1 Sin3Ak-20 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001471 1471 GSM803530 Myers HudsonAlpha SL583 PCR1x 1 exp wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xRawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Sin3Ak-20 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxraPcr1xRawRep2 HepG RXRA PCR1 2 RXRA HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001506 1506 GSM803452 Myers HudsonAlpha SL1054 PCR1x 2 exp wgEncodeHaibTfbsHepg2RxraPcr1xRawRep2 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 RXRA PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxraPcr1xRawRep1 HepG RXRA PCR1 1 RXRA HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001506 1506 GSM803452 Myers HudsonAlpha SL984 PCR1x 1 exp wgEncodeHaibTfbsHepg2RxraPcr1xRawRep1 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 RXRA PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Rad21V0416101RawRep2 HepG RAD21 V101 2 Rad21 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001608 1608 GSM803517 Myers HudsonAlpha SL3586 v041610.1 2 exp wgEncodeHaibTfbsHepg2Rad21V0416101RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 RAD21 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Rad21V0416101RawRep1 HepG RAD21 V101 1 Rad21 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001608 1608 GSM803517 Myers HudsonAlpha SL3179 v041610.1 1 exp wgEncodeHaibTfbsHepg2Rad21V0416101RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 RAD21 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol24h8V0416102RawRep2 HepG Pol2-4H8 V102 2 Pol2-4H8 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002278 2278 GSM1010821 Myers HudsonAlpha SL5604 v041610.2 2 exp wgEncodeHaibTfbsHepg2Pol24h8V0416102RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Pol2-4H8 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol24h8V0416102RawRep1 HepG Pol2-4H8 V102 1 Pol2-4H8 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002278 2278 GSM1010821 Myers HudsonAlpha SL1363 v041610.2 1 exp wgEncodeHaibTfbsHepg2Pol24h8V0416102RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Pol2-4H8 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol2Pcr2xRawRep2 HepG Pol2 PCR2 2 Pol2 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001550 1550 GSM803368 Myers HudsonAlpha SL349 PCR2x 2 exp wgEncodeHaibTfbsHepg2Pol2Pcr2xRawRep2 None RawSignal RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Pol2 PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol2Pcr2xRawRep1 HepG Pol2 PCR2 1 Pol2 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001550 1550 GSM803368 Myers HudsonAlpha SL348 PCR2x 1 exp wgEncodeHaibTfbsHepg2Pol2Pcr2xRawRep1 None RawSignal RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Pol2 PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2P300V0416101RawRep2 HepG p300 V101 2 p300 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001612 1612 GSM803499 Myers HudsonAlpha SL3644 v041610.1 2 exp wgEncodeHaibTfbsHepg2P300V0416101RawRep2 None RawSignal EP300(c-20) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 p300 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2P300V0416101RawRep1 HepG p300 V101 1 p300 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001612 1612 GSM803499 Myers HudsonAlpha SL3154 v041610.1 1 exp wgEncodeHaibTfbsHepg2P300V0416101RawRep1 None RawSignal EP300(c-20) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 p300 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfV0416101RawRep2 HepG NRSF V101 2 NRSF HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002263 2263 GSM1010784 Myers HudsonAlpha SL5897 v041610.1 2 exp wgEncodeHaibTfbsHepg2NrsfV0416101RawRep2 None RawSignal Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NRSF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfV0416101RawRep1 HepG NRSF V101 1 NRSF HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002263 2263 GSM1010784 Myers HudsonAlpha SL5040 v041610.1 1 exp wgEncodeHaibTfbsHepg2NrsfV0416101RawRep1 None RawSignal Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NRSF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfPcr2xRawRep2 HepG NRSF PCR2 2 NRSF HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001549 1549 GSM803344 Myers HudsonAlpha SL274 PCR2x 2 exp wgEncodeHaibTfbsHepg2NrsfPcr2xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NRSF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfPcr2xRawRep1 HepG NRSF PCR2 1 NRSF HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2010-12-14 2011-09-14 wgEncodeEH001549 1549 GSM803344 Myers HudsonAlpha SL273 PCR2x 1 exp wgEncodeHaibTfbsHepg2NrsfPcr2xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NRSF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111RawRep2 HepG NR2F2 V11 2 NR2F2_(SC-271940) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003314 3314 GSM1010810 Myers HudsonAlpha SL16316 v042211.1 2 exp wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111RawRep2 None RawSignal This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NR2F2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111RawRep1 HepG NR2F2 V11 1 NR2F2_(SC-271940) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003314 3314 GSM1010810 Myers HudsonAlpha SL12644 v042211.1 1 exp wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111RawRep1 None RawSignal This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NR2F2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nficsc81335V0422111RawRep2 HepG NFIC V11 2 NFIC_(SC-81335) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002319 2319 GSM1010741 Myers HudsonAlpha SL7554 v042211.1 2 exp wgEncodeHaibTfbsHepg2Nficsc81335V0422111RawRep2 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NFIC v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nficsc81335V0422111RawRep1 HepG NFIC V11 1 NFIC_(SC-81335) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002319 2319 GSM1010741 Myers HudsonAlpha SL7102 v042211.1 1 exp wgEncodeHaibTfbsHepg2Nficsc81335V0422111RawRep1 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 NFIC v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111RawRep2 HepG MYBL2 V11 2 MYBL2_(SC-81192) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002344 2344 GSM1010876 Myers HudsonAlpha SL7564 v042211.1 2 exp wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111RawRep2 None RawSignal The protein encoded by this gene, a member of the MYB family of transcription factor genes, is a nuclear protein involved in cell cycle progression. The encoded protein is phosphorylated by cyclin A/cyclin-dependent kinase 2 during the S-phase of the cell cycle and possesses both activator and repressor activities. It has been shown to activate the cell division cycle 2, cyclin D1, and insulin-like growth factor-binding protein 5 genes. Transcript variants may exist for this gene, but their full-length natures have not been determined. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 MYBL2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111RawRep1 HepG MYBL2 V11 1 MYBL2_(SC-81192) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002344 2344 GSM1010876 Myers HudsonAlpha SL7101 v042211.1 1 exp wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111RawRep1 None RawSignal The protein encoded by this gene, a member of the MYB family of transcription factor genes, is a nuclear protein involved in cell cycle progression. The encoded protein is phosphorylated by cyclin A/cyclin-dependent kinase 2 during the S-phase of the cell cycle and possesses both activator and repressor activities. It has been shown to activate the cell division cycle 2, cyclin D1, and insulin-like growth factor-binding protein 5 genes. Transcript variants may exist for this gene, but their full-length natures have not been determined. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 MYBL2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111RawRep2 HepG MBD4 V11 2 MBD4_(SC-271530) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002318 2318 GSM1010740 Myers HudsonAlpha SL8132 v042211.1 2 exp wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111RawRep2 None RawSignal MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein sequence similarity to bacterial DNA repair enzymes and thus may have some function in DNA repair. Further, MBD4 gene mutations are detected in tumors with primary microsatellite-instability (MSI), a form of genomic instability associated with defective DNA mismatch repair, and MBD4 gene meets 4 of 5 criteria of a bona fide MIS target gene. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 MBD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111RawRep1 HepG MBD4 V11 1 MBD4_(SC-271530) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002318 2318 GSM1010740 Myers HudsonAlpha SL7901 v042211.1 1 exp wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111RawRep1 None RawSignal MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein sequence similarity to bacterial DNA repair enzymes and thus may have some function in DNA repair. Further, MBD4 gene mutations are detected in tumors with primary microsatellite-instability (MSI), a form of genomic instability associated with defective DNA mismatch repair, and MBD4 gene meets 4 of 5 criteria of a bona fide MIS target gene. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 MBD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2MaxV0422111RawRep2 HepG Max V11 2 Max HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003254 3254 GSM1010865 Myers HudsonAlpha SL13292 v042211.1 2 exp wgEncodeHaibTfbsHepg2MaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2MaxV0422111RawRep1 HepG Max V11 1 Max HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003254 3254 GSM1010865 Myers HudsonAlpha SL12422 v042211.1 1 exp wgEncodeHaibTfbsHepg2MaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2JundPcr1xRawRep2 HepG JunD PCR1 2 JunD HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001470 1470 GSM803500 Myers HudsonAlpha SL629 PCR1x 2 exp wgEncodeHaibTfbsHepg2JundPcr1xRawRep2 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 JunD PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2JundPcr1xRawRep1 HepG JunD PCR1 1 JunD HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001470 1470 GSM803500 Myers HudsonAlpha SL635 PCR1x 1 exp wgEncodeHaibTfbsHepg2JundPcr1xRawRep1 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 JunD PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101RawRep2 HepG HNF4G V101 2 HNF4G_(SC-6558) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001651 1651 GSM803404 Myers HudsonAlpha SL3463 v041610.1 2 exp wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101RawRep2 None RawSignal Hepatocyte nuclear factor 4 gamma (HNF4G) also known as NR2A2 (nuclear receptor subfamily 2, group A, member 2) is a nuclear receptor that in humans is encoded by the HNF4G gene hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 HNF4G v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101RawRep1 HepG HNF4G V101 1 HNF4G_(SC-6558) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001651 1651 GSM803404 Myers HudsonAlpha SL3178 v041610.1 1 exp wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101RawRep1 None RawSignal Hepatocyte nuclear factor 4 gamma (HNF4G) also known as NR2A2 (nuclear receptor subfamily 2, group A, member 2) is a nuclear receptor that in humans is encoded by the HNF4G gene hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 HNF4G v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101RawRep2 HepG HNF4A V101 2 HNF4A_(SC-8987) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001595 1595 GSM803460 Myers HudsonAlpha SL2125 v041610.1 2 exp wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101RawRep2 None RawSignal The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 HNF4A v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101RawRep1 HepG HNF4A V101 1 HNF4A_(SC-8987) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001595 1595 GSM803460 Myers HudsonAlpha SL1481 v041610.1 1 exp wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101RawRep1 None RawSignal The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 HNF4A v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101RawRep2 HepG HDAC2 V101 2 HDAC2_(SC-6296) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001618 1618 GSM803493 Myers HudsonAlpha SL3583 v041610.1 2 exp wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101RawRep2 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 HDAC2 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101RawRep1 HepG HDAC2 V101 1 HDAC2_(SC-6296) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001618 1618 GSM803493 Myers HudsonAlpha SL3177 v041610.1 1 exp wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101RawRep1 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 HDAC2 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2GabpPcr2xRawRep2 HepG GABP PCR2 2 GABP HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001548 1548 GSM803343 Myers HudsonAlpha SL276 PCR2x 2 exp wgEncodeHaibTfbsHepg2GabpPcr2xRawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 GABP PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2GabpPcr2xRawRep1 HepG GABP PCR2 1 GABP HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001548 1548 GSM803343 Myers HudsonAlpha SL275 PCR2x 1 exp wgEncodeHaibTfbsHepg2GabpPcr2xRawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 GABP PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101RawRep2 HepG FOXA2 V101 2 FOXA2_(SC-6554) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001650 1650 GSM803403 Myers HudsonAlpha SL3175 v041610.1 2 exp wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101RawRep2 None RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOXA2 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101RawRep1 HepG FOXA2 V101 1 FOXA2_(SC-6554) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001650 1650 GSM803403 Myers HudsonAlpha SL2196 v041610.1 1 exp wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101RawRep1 None RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOXA2 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101RawRep2 HepG FOXA1 V101 2 FOXA1_(SC-6553) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001594 1594 GSM803461 Myers HudsonAlpha SL2124 v041610.1 2 exp wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101RawRep2 None RawSignal This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOXA1 6553 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101RawRep1 HepG FOXA1 V101 1 FOXA1_(SC-6553) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001594 1594 GSM803461 Myers HudsonAlpha SL1786 v041610.1 1 exp wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101RawRep1 None RawSignal This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOXA1 6553 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101RawRep2 HepG FOXA1 V101 2 FOXA1_(SC-101058) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001630 1630 GSM803432 Myers HudsonAlpha SL2194 v041610.1 2 exp wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101RawRep2 None RawSignal This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOXA1 101058 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101RawRep1 HepG FOXA1 V101 1 FOXA1_(SC-101058) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001630 1630 GSM803432 Myers HudsonAlpha SL1788 v041610.1 1 exp wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101RawRep1 None RawSignal This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOXA1 101058 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Fosl2V0416101RawRep2 HepG FOSL2 V101 2 FOSL2 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001501 1501 GSM803451 Myers HudsonAlpha SL1107 v041610.1 2 exp wgEncodeHaibTfbsHepg2Fosl2V0416101RawRep2 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOSL2 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Fosl2V0416101RawRep1 HepG FOSL2 V101 1 FOSL2 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001501 1501 GSM803451 Myers HudsonAlpha SL632 v041610.1 1 exp wgEncodeHaibTfbsHepg2Fosl2V0416101RawRep1 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 FOSL2 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Elf1sc631V0416101RawRep2 HepG ELF1 V101 2 ELF1_(SC-631) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001641 1641 GSM803415 Myers HudsonAlpha SL3986 v041610.1 2 exp wgEncodeHaibTfbsHepg2Elf1sc631V0416101RawRep2 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ELF1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Elf1sc631V0416101RawRep1 HepG ELF1 V101 1 ELF1_(SC-631) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001641 1641 GSM803415 Myers HudsonAlpha SL3645 v041610.1 1 exp wgEncodeHaibTfbsHepg2Elf1sc631V0416101RawRep1 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ELF1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101RawRep2 HepG CTCF V101 2 CTCF_(SC-5916) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2010-01-06 2010-10-06 wgEncodeEH001516 1516 GSM803486 Myers HudsonAlpha SL3582 v041610.1 2 exp wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101RawRep2 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CTCF 5916 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101RawRep1 HepG CTCF V101 1 CTCF_(SC-5916) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2010-01-06 2010-10-06 wgEncodeEH001516 1516 GSM803486 Myers HudsonAlpha SL3176 v041610.1 1 exp wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101RawRep1 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CTCF 5916 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Creb1sc240V0422111RawRep2 HepG CREB1 V11 2 CREB1_(SC-240) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003312 3312 GSM1010808 Myers HudsonAlpha SL13290 v042211.1 2 exp wgEncodeHaibTfbsHepg2Creb1sc240V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CREB1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Creb1sc240V0422111RawRep1 HepG CREB1 V11 1 CREB1_(SC-240) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003312 3312 GSM1010808 Myers HudsonAlpha SL12405 v042211.1 1 exp wgEncodeHaibTfbsHepg2Creb1sc240V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CREB1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpdsc636V0416101RawRep2 HepG CEBPD V101 2 CEBPD_(SC-636) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002305 2305 GSM1010777 Myers HudsonAlpha SL4940 v041610.1 2 exp wgEncodeHaibTfbsHepg2Cebpdsc636V0416101RawRep2 None RawSignal The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CEBPD v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpdsc636V0416101RawRep1 HepG CEBPD V101 1 CEBPD_(SC-636) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002305 2305 GSM1010777 Myers HudsonAlpha SL4210 v041610.1 1 exp wgEncodeHaibTfbsHepg2Cebpdsc636V0416101RawRep1 None RawSignal The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CEBPD v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpbsc150V0416101RawRep2 HepG CEBPB V101 2 CEBPB_(SC-150) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002304 2304 GSM1010778 Myers HudsonAlpha SL4939 v041610.1 2 exp wgEncodeHaibTfbsHepg2Cebpbsc150V0416101RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CEBPB v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpbsc150V0416101RawRep1 HepG CEBPB V101 1 CEBPB_(SC-150) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002304 2304 GSM1010778 Myers HudsonAlpha SL4209 v041610.1 1 exp wgEncodeHaibTfbsHepg2Cebpbsc150V0416101RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CEBPB v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Bhlhe40V0416101RawRep2 HepG BHLHE40 2 BHLHE40 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001515 1515 GSM803483 Myers HudsonAlpha SL3460 v041610.1 2 exp wgEncodeHaibTfbsHepg2Bhlhe40V0416101RawRep2 None RawSignal This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 BHLHE40 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Bhlhe40V0416101RawRep1 HepG BHLHE40 1 BHLHE40 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001515 1515 GSM803483 Myers HudsonAlpha SL1059 v041610.1 1 exp wgEncodeHaibTfbsHepg2Bhlhe40V0416101RawRep1 None RawSignal This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 BHLHE40 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Atf3V0416101RawRep2 HepG ATF3 V101 2 ATF3 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001568 1568 GSM803503 Myers HudsonAlpha SL1787 v041610.1 2 exp wgEncodeHaibTfbsHepg2Atf3V0416101RawRep2 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ATF3 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Atf3V0416101RawRep1 HepG ATF3 V101 1 ATF3 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001568 1568 GSM803503 Myers HudsonAlpha SL2386 v041610.1 1 exp wgEncodeHaibTfbsHepg2Atf3V0416101RawRep1 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 ATF3 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3RxlchPcr1xRawRep1 HeLa RvXL PCR1 1 RevXlinkChromatin HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001628 1628 GSM803479 Myers HudsonAlpha SL592 PCR1x 1 input wgEncodeHaibTfbsHelas3RxlchPcr1xRawRep1 None RawSignal cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Taf1Pcr1xRawRep2 HeLa TAF1 PCR1 2 TAF1 HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001505 1505 GSM803455 Myers HudsonAlpha SL706 PCR1x 2 exp wgEncodeHaibTfbsHelas3Taf1Pcr1xRawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 TAF1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Taf1Pcr1xRawRep1 HeLa TAF1 PCR1 1 TAF1 HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001505 1505 GSM803455 Myers HudsonAlpha SL590 PCR1x 1 exp wgEncodeHaibTfbsHelas3Taf1Pcr1xRawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 TAF1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Pol2Pcr1xRawRep2 HeLa Pol2 PCR1 2 Pol2 HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001474 1474 GSM803533 Myers HudsonAlpha SL672 PCR1x 2 exp wgEncodeHaibTfbsHelas3Pol2Pcr1xRawRep2 None RawSignal RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 Pol2 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Pol2Pcr1xRawRep1 HeLa Pol2 PCR1 1 Pol2 HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001474 1474 GSM803533 Myers HudsonAlpha SL631 PCR1x 1 exp wgEncodeHaibTfbsHelas3Pol2Pcr1xRawRep1 None RawSignal RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 Pol2 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3NrsfPcr1xRawRep2 HeLa NRSF PCR1 2 NRSF HeLa-S3 ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001629 1629 GSM803478 Myers HudsonAlpha SL1322 PCR1x 2 exp wgEncodeHaibTfbsHelas3NrsfPcr1xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 NRSF PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3NrsfPcr1xRawRep1 HeLa NRSF PCR1 1 NRSF HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001629 1629 GSM803478 Myers HudsonAlpha SL679 PCR1x 1 exp wgEncodeHaibTfbsHelas3NrsfPcr1xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 NRSF PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3GabpPcr1xRawRep2 HeLa GABP PCR1 2 GABP HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001504 1504 GSM803454 Myers HudsonAlpha SL611 PCR1x 2 exp wgEncodeHaibTfbsHelas3GabpPcr1xRawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 GABP PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3GabpPcr1xRawRep1 HeLa GABP PCR1 1 GABP HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001504 1504 GSM803454 Myers HudsonAlpha SL610 PCR1x 1 exp wgEncodeHaibTfbsHelas3GabpPcr1xRawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 GABP PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsRxlchV0422111RawRep2 H1-neu RvXL 2 RevXlinkChromatin H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003425 3425 GSM1010873 Myers HudsonAlpha SL16755 v042211.1 2 input wgEncodeHaibTfbsH1neuronsRxlchV0422111RawRep2 None RawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsRxlchV0422111RawRep1 H1-neu RvXL 1 RevXlinkChromatin H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003425 3425 GSM1010873 Myers HudsonAlpha SL13320 v042211.1 1 input wgEncodeHaibTfbsH1neuronsRxlchV0422111RawRep1 None RawSignal neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsTaf1V0422111RawRep2 H1-neu TAF1 2 TAF1 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003266 3266 GSM1010805 Myers HudsonAlpha SL14594 v042211.1 2 exp wgEncodeHaibTfbsH1neuronsTaf1V0422111RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons TAF1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsTaf1V0422111RawRep1 H1-neu TAF1 1 TAF1 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003266 3266 GSM1010805 Myers HudsonAlpha SL13300 v042211.1 1 exp wgEncodeHaibTfbsH1neuronsTaf1V0422111RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons TAF1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsPol24h8V0422111RawRep2 H1-neu Pol2-4H8 2 Pol2-4H8 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003265 3265 GSM1010803 Myers HudsonAlpha SL14592 v042211.1 2 exp wgEncodeHaibTfbsH1neuronsPol24h8V0422111RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons Pol2-4H8 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsPol24h8V0422111RawRep1 H1-neu Pol2-4H8 1 Pol2-4H8 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003265 3265 GSM1010803 Myers HudsonAlpha SL13298 v042211.1 1 exp wgEncodeHaibTfbsH1neuronsPol24h8V0422111RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons Pol2-4H8 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsNrsfV0422111RawRep2 H1-neu NRSF 2 NRSF H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003264 3264 GSM1010804 Myers HudsonAlpha SL14593 v042211.1 2 exp wgEncodeHaibTfbsH1neuronsNrsfV0422111RawRep2 None RawSignal Neuron-restrictive silencer transcription factor neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons NRSF v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsNrsfV0422111RawRep1 H1-neu NRSF 1 NRSF H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003264 3264 GSM1010804 Myers HudsonAlpha SL13299 v042211.1 1 exp wgEncodeHaibTfbsH1neuronsNrsfV0422111RawRep1 None RawSignal Neuron-restrictive silencer transcription factor neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-neurons NRSF v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchV0422111RawRep3 A549 RvXL V11 3 RevXlinkChromatin A549 ChipSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEH003423 3423 GSM1010866 Myers HudsonAlpha SL12790 v042211.1 3 input wgEncodeHaibTfbsA549RxlchV0422111RawRep3 None RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control v042211.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchV0422111RawRep2 A549 RvXL V11 2 RevXlinkChromatin A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003423 3423 GSM1010866 Myers HudsonAlpha SL16753 v042211.1 2 input wgEncodeHaibTfbsA549RxlchV0422111RawRep2 None RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchV0422111RawRep1 A549 RvXL V11 1 RevXlinkChromatin A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003423 3423 GSM1010866 Myers HudsonAlpha SL13321 v042211.1 1 input wgEncodeHaibTfbsA549RxlchV0422111RawRep1 None RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchV0422111Etoh02RawRep1 A549 RX Eth V11 1 RevXlinkChromatin A549 ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002273 2273 GSM1010818 Myers HudsonAlpha SL6021 v042211.1 1 input wgEncodeHaibTfbsA549RxlchV0422111Etoh02RawRep1 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchV0416101Etoh02RawRep1 A549 RvXL V101 1 RevXlinkChromatin A549 ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002283 2283 GSM1010795 Myers HudsonAlpha SL3978 v041610.1 1 input wgEncodeHaibTfbsA549RxlchV0416101Etoh02RawRep1 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control EtOH v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchPcr2xEtoh02RawRep1 A549 RX Eth PC2 1 RevXlinkChromatin A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001589 1589 GSM803435 Myers HudsonAlpha SL307 PCR2x 1 input wgEncodeHaibTfbsA549RxlchPcr2xEtoh02RawRep1 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control EtOH PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchPcr1xEtoh02RawRep1 A549 RX Eth PC1 1 RevXlinkChromatin A549 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001644 1644 GSM803412 Myers HudsonAlpha SL475 PCR1x 1 input wgEncodeHaibTfbsA549RxlchPcr1xEtoh02RawRep1 EtOH_0.02pct RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control EtOH PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchPcr2xDex100nmRawRep1 A549 RX DEX PC2 1 RevXlinkChromatin A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001590 1590 GSM803465 Myers HudsonAlpha SL335 PCR2x 1 input wgEncodeHaibTfbsA549RxlchPcr2xDex100nmRawRep1 DEX_100nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control DEX 100nM PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549RxlchPcr1xDex100nmRawRep1 A549 RX DEX PC1 1 RevXlinkChromatin A549 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001643 1643 GSM803417 Myers HudsonAlpha SL474 PCR1x 1 input wgEncodeHaibTfbsA549RxlchPcr1xDex100nmRawRep1 DEX_100nM RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Control DEX 100nM PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02RawRep2 A549 ZBTB33 ETH 2 ZBTB33 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002295 2295 GSM1010832 Myers HudsonAlpha SL6592 v042211.1 2 exp wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ZBTB33 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02RawRep1 A549 ZBTB33 ETH 1 ZBTB33 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002295 2295 GSM1010832 Myers HudsonAlpha SL6016 v042211.1 1 exp wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ZBTB33 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Yy1cV0422111Etoh02RawRep2 A549 YY1 EtOH 2 YY1_(SC-281) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002282 2282 GSM1010794 Myers HudsonAlpha SL5699 v042211.1 2 exp wgEncodeHaibTfbsA549Yy1cV0422111Etoh02RawRep2 EtOH_0.02pct RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 YY1 281 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Yy1cV0422111Etoh02RawRep1 A549 YY1 EtOH 1 YY1_(SC-281) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002282 2282 GSM1010794 Myers HudsonAlpha SL5357 v042211.1 1 exp wgEncodeHaibTfbsA549Yy1cV0422111Etoh02RawRep1 EtOH_0.02pct RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 YY1 281 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1V0422111Etoh02RawRep2 A549 USF Et V11 2 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002291 2291 GSM1010828 Myers HudsonAlpha SL7279 v042211.1 2 exp wgEncodeHaibTfbsA549Usf1V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 USF-1 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1V0422111Etoh02RawRep1 A549 USF Et V11 1 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002291 2291 GSM1010828 Myers HudsonAlpha SL6593 v042211.1 1 exp wgEncodeHaibTfbsA549Usf1V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 USF-1 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02RawRep2 A549 USF1 Et P1 2 USF-1 A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001539 1539 GSM803429 Myers HudsonAlpha SL1207 PCR1x 2 exp wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02RawRep2 EtOH_0.02pct RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 USF-1 EtOH PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02RawRep1 A549 USF1 Et P1 1 USF-1 A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001539 1539 GSM803429 Myers HudsonAlpha SL1080 PCR1x 1 exp wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02RawRep1 EtOH_0.02pct RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 USF-1 EtOH PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmRawRep2 A549 USF1 DEX 2 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001509 1509 GSM803457 Myers HudsonAlpha SL1206 PCR1x 2 exp wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmRawRep2 DEX_100nM RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 USF-1 DEX 100nM PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmRawRep1 A549 USF1 DEX 1 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001509 1509 GSM803457 Myers HudsonAlpha SL1079 PCR1x 1 exp wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmRawRep1 DEX_100nM RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 USF-1 DEX 100nM PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tead4sc101184V0422111RawRep2 A549 TEAD4 V11 2 TEAD4_(SC-101184) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003273 3273 GSM1010868 Myers HudsonAlpha SL14702 v042211.1 2 exp wgEncodeHaibTfbsA549Tead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tead4sc101184V0422111RawRep1 A549 TEAD4 V11 1 TEAD4_(SC-101184) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003273 3273 GSM1010868 Myers HudsonAlpha SL13479 v042211.1 1 exp wgEncodeHaibTfbsA549Tead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tcf12V0422111Etoh02RawRep2 A549 TCF12 EtOH 2 TCF12 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002312 2312 GSM1010746 Myers HudsonAlpha SL8076 v042211.1 2 exp wgEncodeHaibTfbsA549Tcf12V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 TCF12 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tcf12V0422111Etoh02RawRep1 A549 TCF12 EtOH 1 TCF12 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002312 2312 GSM1010746 Myers HudsonAlpha SL7114 v042211.1 1 exp wgEncodeHaibTfbsA549Tcf12V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 TCF12 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Taf1V0422111Etoh02RawRep2 A549 TAF1 EtOH 2 TAF1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002275 2275 GSM1010812 Myers HudsonAlpha SL5700 v042211.1 2 exp wgEncodeHaibTfbsA549Taf1V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 TAF1 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Taf1V0422111Etoh02RawRep1 A549 TAF1 EtOH 1 TAF1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002275 2275 GSM1010812 Myers HudsonAlpha SL5358 v042211.1 1 exp wgEncodeHaibTfbsA549Taf1V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 TAF1 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sp1V0422111Etoh02RawRep2 A549 SP1 EtOH 2 SP1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002274 2274 GSM1010813 Myers HudsonAlpha SL5701 v042211.1 2 exp wgEncodeHaibTfbsA549Sp1V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 SP1 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sp1V0422111Etoh02RawRep1 A549 SP1 EtOH 1 SP1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002274 2274 GSM1010813 Myers HudsonAlpha SL5360 v042211.1 1 exp wgEncodeHaibTfbsA549Sp1V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 SP1 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Six5V0422111Etoh02RawRep2 A549 SIX5 EtOH 2 SIX5 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002341 2341 GSM1010879 Myers HudsonAlpha SL8400 v042211.1 2 exp wgEncodeHaibTfbsA549Six5V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 SIX5 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Six5V0422111Etoh02RawRep1 A549 SIX5 EtOH 1 SIX5 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002341 2341 GSM1010879 Myers HudsonAlpha SL7277 v042211.1 1 exp wgEncodeHaibTfbsA549Six5V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 SIX5 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02RawRep2 A549 Sin3A EtOH 2 Sin3Ak-20 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002342 2342 GSM1010882 Myers HudsonAlpha SL8401 v042211.1 2 exp wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Sin3Ak-20 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02RawRep1 A549 Sin3A EtOH 1 Sin3Ak-20 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002342 2342 GSM1010882 Myers HudsonAlpha SL7275 v042211.1 1 exp wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Sin3Ak-20 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Rad21V0422111RawRep2 A549 RAD21 V11 2 Rad21 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003272 3272 GSM1010761 Myers HudsonAlpha SL16300 v042211.1 2 exp wgEncodeHaibTfbsA549Rad21V0422111RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 RAD21 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Rad21V0422111RawRep1 A549 RAD21 V11 1 Rad21 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003272 3272 GSM1010761 Myers HudsonAlpha SL12634 v042211.1 1 exp wgEncodeHaibTfbsA549Rad21V0422111RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 RAD21 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02RawRep2 A549 Pol2 EtOH 2 Pol2 A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001493 1493 GSM803360 Myers HudsonAlpha SL334 PCR2x 2 exp wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02RawRep2 EtOH_0.02pct RawSignal RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Pol2 EtOH PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02RawRep1 A549 Pol2 EtOH 1 Pol2 A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001493 1493 GSM803360 Myers HudsonAlpha SL245 PCR2x 1 exp wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02RawRep1 EtOH_0.02pct RawSignal RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Pol2 EtOH PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmRawRep2 A549 Pol2 DEX 2 Pol2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2010-12-20 2011-09-20 wgEncodeEH001494 1494 GSM803361 Myers HudsonAlpha SL306 PCR2x 2 exp wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmRawRep2 DEX_100nM RawSignal RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Pol2 DEX 100nM PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmRawRep1 A549 Pol2 DEX 1 Pol2 A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001494 1494 GSM803361 Myers HudsonAlpha SL244 PCR2x 1 exp wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmRawRep1 DEX_100nM RawSignal RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Pol2 DEX 100nM PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pbx3V0422111RawRep2 A549 PBx3 V11 2 Pbx3 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003255 3255 GSM1010755 Myers HudsonAlpha SL16043 v042211.1 2 exp wgEncodeHaibTfbsA549Pbx3V0422111RawRep2 None RawSignal Pbx 3 (D-17) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 PBx3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pbx3V0422111RawRep1 A549 PBx3 V11 1 Pbx3 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003255 3255 GSM1010755 Myers HudsonAlpha SL13476 v042211.1 1 exp wgEncodeHaibTfbsA549Pbx3V0422111RawRep1 None RawSignal Pbx 3 (D-17) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 PBx3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549P300V0422111Etoh02RawRep2 A549 p300 EtOH 2 p300 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002292 2292 GSM1010827 Myers HudsonAlpha SL7115 v042211.1 2 exp wgEncodeHaibTfbsA549P300V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal EP300(c-20) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 p300 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549P300V0422111Etoh02RawRep1 A549 p300 EtOH 1 p300 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002292 2292 GSM1010827 Myers HudsonAlpha SL6437 v042211.1 1 exp wgEncodeHaibTfbsA549P300V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal EP300(c-20) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 p300 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549NrsfV0422111Etoh02RawRep2 A549 NRSF EtOH 2 NRSF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002311 2311 GSM1010749 Myers HudsonAlpha SL8075 v042211.1 2 exp wgEncodeHaibTfbsA549NrsfV0422111Etoh02RawRep2 EtOH_0.02pct RawSignal Neuron-restrictive silencer transcription factor epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 NRSF EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549NrsfV0422111Etoh02RawRep1 A549 NRSF EtOH 1 NRSF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002311 2311 GSM1010749 Myers HudsonAlpha SL7110 v042211.1 1 exp wgEncodeHaibTfbsA549NrsfV0422111Etoh02RawRep1 EtOH_0.02pct RawSignal Neuron-restrictive silencer transcription factor epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 NRSF EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549MaxV0422111RawRep2 A549 Max V11 2 Max A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003251 3251 GSM1010728 Myers HudsonAlpha SL13754 v042211.1 2 exp wgEncodeHaibTfbsA549MaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549MaxV0422111RawRep1 A549 Max V11 1 Max A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003251 3251 GSM1010728 Myers HudsonAlpha SL12638 v042211.1 1 exp wgEncodeHaibTfbsA549MaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549JundV0416102Etoh02RawRep2 A549 JunD EtOH 2 JunD A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002327 2327 GSM1010723 Myers HudsonAlpha SL4698 v041610.2 2 exp wgEncodeHaibTfbsA549JundV0416102Etoh02RawRep2 EtOH_0.02pct RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 JunD EtOH v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549JundV0416102Etoh02RawRep1 A549 JunD EtOH 1 JunD A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002327 2327 GSM1010723 Myers HudsonAlpha SL3900 v041610.2 1 exp wgEncodeHaibTfbsA549JundV0416102Etoh02RawRep1 EtOH_0.02pct RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 JunD EtOH v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr2xEtoh02RawRep2 A549 GR Eth PC2 2 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001557 1557 GSM803373 Myers HudsonAlpha SL305 PCR2x 2 input wgEncodeHaibTfbsA549GrPcr2xEtoh02RawRep2 EtOH_0.02pct RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR EtOH PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr2xEtoh02RawRep1 A549 GR Eth PC2 1 GR A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001557 1557 GSM803373 Myers HudsonAlpha SL247 PCR2x 1 input wgEncodeHaibTfbsA549GrPcr2xEtoh02RawRep1 EtOH_0.02pct RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR EtOH PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xEtoh02RawRep2 A549 GR Eth PC1 2 GR A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001526 1526 GSM803395 Myers HudsonAlpha SL879 PCR1x 2 input wgEncodeHaibTfbsA549GrPcr1xEtoh02RawRep2 EtOH_0.02pct RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR EtOH PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xEtoh02RawRep1 A549 GR Eth PC1 1 GR A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001526 1526 GSM803395 Myers HudsonAlpha SL878 PCR1x 1 input wgEncodeHaibTfbsA549GrPcr1xEtoh02RawRep1 EtOH_0.02pct RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR EtOH PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex5nmRawRep2 A549 GR DX5nM 2 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001492 1492 GSM803359 Myers HudsonAlpha SL881 PCR1x 2 exp wgEncodeHaibTfbsA549GrPcr1xDex5nmRawRep2 DEX_5nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 5 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 5nM PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex5nmRawRep1 A549 GR DX5nM 1 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001492 1492 GSM803359 Myers HudsonAlpha SL880 PCR1x 1 exp wgEncodeHaibTfbsA549GrPcr1xDex5nmRawRep1 DEX_5nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 5 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 5nM PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex50nmRawRep2 A549 GR DX50nM 2 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001491 1491 GSM803358 Myers HudsonAlpha SL883 PCR1x 2 exp wgEncodeHaibTfbsA549GrPcr1xDex50nmRawRep2 DEX_50nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 50 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 50nM PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex50nmRawRep1 A549 GR DX50nM 1 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001491 1491 GSM803358 Myers HudsonAlpha SL882 PCR1x 1 exp wgEncodeHaibTfbsA549GrPcr1xDex50nmRawRep1 DEX_50nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 50 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 50nM PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex500pmRawRep2 A549 GR DX.5nM 2 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001490 1490 GSM803357 Myers HudsonAlpha SL885 PCR1x 2 exp wgEncodeHaibTfbsA549GrPcr1xDex500pmRawRep2 DEX_500pM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 500 pM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 500pM PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex500pmRawRep1 A549 GR DX.5nM 1 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001490 1490 GSM803357 Myers HudsonAlpha SL884 PCR1x 1 exp wgEncodeHaibTfbsA549GrPcr1xDex500pmRawRep1 DEX_500pM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 500 pM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 500pM PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr2xDex100nmRawRep2 A549 GR DX100nM 2 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001555 1555 GSM803371 Myers HudsonAlpha SL304 PCR2x 2 exp wgEncodeHaibTfbsA549GrPcr2xDex100nmRawRep2 DEX_100nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 100nM PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr2xDex100nmRawRep1 A549 GR DX100nM 1 GR A549 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001555 1555 GSM803371 Myers HudsonAlpha SL246 PCR2x 1 exp wgEncodeHaibTfbsA549GrPcr2xDex100nmRawRep1 DEX_100nM RawSignal Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GR DEX 100nM PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Gata3V0422111RawRep2 A549 GATA3 V11 2 GATA3_(SC-268) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003250 3250 GSM1010727 Myers HudsonAlpha SL13283 v042211.1 2 exp wgEncodeHaibTfbsA549Gata3V0422111RawRep2 None RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GATA3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Gata3V0422111RawRep1 A549 GATA3 V11 1 GATA3_(SC-268) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003250 3250 GSM1010727 Myers HudsonAlpha SL12399 v042211.1 1 exp wgEncodeHaibTfbsA549Gata3V0422111RawRep1 None RawSignal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GATA3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GabpV0422111Etoh02RawRep2 A549 GABP EtOH 2 GABP A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002294 2294 GSM1010833 Myers HudsonAlpha SL6595 v042211.1 2 exp wgEncodeHaibTfbsA549GabpV0422111Etoh02RawRep2 EtOH_0.02pct RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GABP EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GabpV0422111Etoh02RawRep1 A549 GABP EtOH 1 GABP A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002294 2294 GSM1010833 Myers HudsonAlpha SL6015 v042211.1 1 exp wgEncodeHaibTfbsA549GabpV0422111Etoh02RawRep1 EtOH_0.02pct RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 GABP EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa2V0416102Etoh02RawRep2 A549 FOXA2 EtOH 2 FOXA2_(SC-6554) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002326 2326 GSM1010724 Myers HudsonAlpha SL3253 v041610.2 2 exp wgEncodeHaibTfbsA549Foxa2V0416102Etoh02RawRep2 EtOH_0.02pct RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOXA2 EtOH v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa2V0416102Etoh02RawRep1 A549 FOXA2 EtOH 1 FOXA2_(SC-6554) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002326 2326 GSM1010724 Myers HudsonAlpha SL3077 v041610.2 1 exp wgEncodeHaibTfbsA549Foxa2V0416102Etoh02RawRep1 EtOH_0.02pct RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOXA2 EtOH v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa1V0416102Etoh02RawRep2 A549 FOXA1 EtOH 2 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002325 2325 GSM1010725 Myers HudsonAlpha SL3251 v041610.2 2 input wgEncodeHaibTfbsA549Foxa1V0416102Etoh02RawRep2 EtOH_0.02pct RawSignal This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOXA1 101058 EtOH v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa1V0416102Etoh02RawRep1 A549 FOXA1 EtOH 1 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002325 2325 GSM1010725 Myers HudsonAlpha SL2665 v041610.2 1 input wgEncodeHaibTfbsA549Foxa1V0416102Etoh02RawRep1 EtOH_0.02pct RawSignal This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOXA1 101058 EtOH v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmRawRep2 A549 FOXA1 DEX 2 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002293 2293 GSM1010826 Myers HudsonAlpha SL3250 v041610.2 2 exp wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmRawRep2 DEX_100nM RawSignal This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOXA1 101058 DEX 100nM v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmRawRep1 A549 FOXA1 DEX 1 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002293 2293 GSM1010826 Myers HudsonAlpha SL2666 v041610.2 1 exp wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmRawRep1 DEX_100nM RawSignal This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOXA1 101058 DEX 100nM v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Fosl2V0422111Etoh02RawRep2 A549 FOSL2 EtOH 2 FOSL2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002310 2310 GSM1010748 Myers HudsonAlpha SL8077 v042211.1 2 exp wgEncodeHaibTfbsA549Fosl2V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOSL2 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Fosl2V0422111Etoh02RawRep1 A549 FOSL2 EtOH 1 FOSL2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002310 2310 GSM1010748 Myers HudsonAlpha SL7116 v042211.1 1 exp wgEncodeHaibTfbsA549Fosl2V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 FOSL2 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ets1V0422111Etoh02RawRep2 A549 ETS1 EtOH 2 ETS1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002290 2290 GSM1010829 Myers HudsonAlpha SL7108 v042211.1 2 exp wgEncodeHaibTfbsA549Ets1V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ETS1 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ets1V0422111Etoh02RawRep1 A549 ETS1 EtOH 1 ETS1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002290 2290 GSM1010829 Myers HudsonAlpha SL6600 v042211.1 1 exp wgEncodeHaibTfbsA549Ets1V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ETS1 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Elf1V0422111Etoh02RawRep2 A549 ELF1 EtOH 2 ELF1_(SC-631) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002289 2289 GSM1010790 Myers HudsonAlpha SL7113 v042211.1 2 exp wgEncodeHaibTfbsA549Elf1V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ELF1 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Elf1V0422111Etoh02RawRep1 A549 ELF1 EtOH 1 ELF1_(SC-631) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002289 2289 GSM1010790 Myers HudsonAlpha SL6436 v042211.1 1 exp wgEncodeHaibTfbsA549Elf1V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ELF1 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549E2f6V0422111RawRep2 A549 E2F6 V11 2 E2F6 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003244 3244 GSM1010766 Myers HudsonAlpha SL14581 v042211.1 2 exp wgEncodeHaibTfbsA549E2f6V0422111RawRep2 None RawSignal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 E2F6 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549E2f6V0422111RawRep1 A549 E2F6 V11 1 E2F6 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003244 3244 GSM1010766 Myers HudsonAlpha SL13319 v042211.1 1 exp wgEncodeHaibTfbsA549E2f6V0422111RawRep1 None RawSignal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 E2F6 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02RawRep2 A549 CTCF EtOH 2 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001508 1508 GSM803456 Myers HudsonAlpha SL1078 PCR1x 2 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02RawRep2 EtOH_0.02pct RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CTCF 5916 EtOH PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02RawRep1 A549 CTCF EtOH 1 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001508 1508 GSM803456 Myers HudsonAlpha SL1205 PCR1x 1 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02RawRep1 EtOH_0.02pct RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CTCF 5916 EtOH PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmRawRep2 A549 CTCF DEX 2 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001507 1507 GSM803453 Myers HudsonAlpha SL1077 PCR1x 2 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmRawRep2 DEX_100nM RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CTCF 5916 DEX 100nM PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmRawRep1 A549 CTCF DEX 1 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001507 1507 GSM803453 Myers HudsonAlpha SL1204 PCR1x 1 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmRawRep1 DEX_100nM RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CTCF 5916 DEX 100nM PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Creb1sc240V0416102Etoh02RawRep2 A549 CREB1 EtOH 2 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002324 2324 GSM1010726 Myers HudsonAlpha SL3898 v041610.2 2 input wgEncodeHaibTfbsA549Creb1sc240V0416102Etoh02RawRep2 EtOH_0.02pct RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CREB1 EtOH v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Creb1sc240Pcr1xEtoh02RawRep1 A549 CREB1 EtOH 1 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002322 2322 GSM1010720 Myers HudsonAlpha SL1668 PCR1x 1 input wgEncodeHaibTfbsA549Creb1sc240Pcr1xEtoh02RawRep1 EtOH_0.02pct RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CREB1 EtOH PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmRawRep2 A549 CREB1 DEX 2 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002323 2323 GSM1010719 Myers HudsonAlpha SL3897 v041610.2 2 exp wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmRawRep2 DEX_100nM RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CREB1 DEX 100nM v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmRawRep1 A549 CREB1 DEX 1 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002323 2323 GSM1010719 Myers HudsonAlpha SL1667 v041610.2 1 exp wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmRawRep1 DEX_100nM RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CREB1 DEX 100nM v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Cebpbsc150V0422111RawRep2 A549 CEBPB V11 2 CEBPB_(SC-150) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003271 3271 GSM1010871 Myers HudsonAlpha SL16299 v042211.1 2 exp wgEncodeHaibTfbsA549Cebpbsc150V0422111RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CEBPB v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Cebpbsc150V0422111RawRep1 A549 CEBPB V11 1 CEBPB_(SC-150) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003271 3271 GSM1010871 Myers HudsonAlpha SL12637 v042211.1 1 exp wgEncodeHaibTfbsA549Cebpbsc150V0422111RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CEBPB v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Bcl3V0422111Etoh02RawRep2 A549 BCL3 EtOH 2 BCL3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002303 2303 GSM1010775 Myers HudsonAlpha SL7109 v042211.1 2 exp wgEncodeHaibTfbsA549Bcl3V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 BCL3 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Bcl3V0422111Etoh02RawRep1 A549 BCL3 EtOH 1 BCL3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002303 2303 GSM1010775 Myers HudsonAlpha SL6596 v042211.1 1 exp wgEncodeHaibTfbsA549Bcl3V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 BCL3 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Atf3V0422111Etoh02RawRep2 A549 ATF3 EtOH 2 ATF3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002288 2288 GSM1010789 Myers HudsonAlpha SL7273 v042211.1 2 exp wgEncodeHaibTfbsA549Atf3V0422111Etoh02RawRep2 EtOH_0.02pct RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ATF3 EtOH v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Atf3V0422111Etoh02RawRep1 A549 ATF3 EtOH 1 ATF3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002288 2288 GSM1010789 Myers HudsonAlpha SL6010 v042211.1 1 exp wgEncodeHaibTfbsA549Atf3V0422111Etoh02RawRep1 EtOH_0.02pct RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 ATF3 EtOH v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchV0422111RawRep4 K562 RvXL V11 4 RevXlinkChromatin K562 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH002332 2332 GSM1010894 Myers HudsonAlpha SL12793 v042211.1 4 input wgEncodeHaibTfbsK562RxlchV0422111RawRep4 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control v042211.1 ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchV0422111RawRep3 K562 RvXL V11 3 RevXlinkChromatin K562 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH002332 2332 GSM1010894 Myers HudsonAlpha SL11659 v042211.1 3 input wgEncodeHaibTfbsK562RxlchV0422111RawRep3 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control v042211.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchV0422111RawRep2 K562 RvXL V11 2 RevXlinkChromatin K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002332 2332 GSM1010894 Myers HudsonAlpha SL9103 v042211.1 2 input wgEncodeHaibTfbsK562RxlchV0422111RawRep2 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchV0422111RawRep1 K562 RvXL V11 1 RevXlinkChromatin K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002332 2332 GSM1010894 Myers HudsonAlpha SL6023 v042211.1 1 input wgEncodeHaibTfbsK562RxlchV0422111RawRep1 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchV0416101RawRep2 K562 RvXL V101 2 RevXlinkChromatin K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001599 1599 GSM803468 Myers HudsonAlpha SL3980 v041610.1 2 input wgEncodeHaibTfbsK562RxlchV0416101RawRep2 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchV0416101RawRep1 K562 RvXL V101 1 RevXlinkChromatin K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001599 1599 GSM803468 Myers HudsonAlpha SL2455 v041610.1 1 input wgEncodeHaibTfbsK562RxlchV0416101RawRep1 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchPcr1xRawRep4 K562 RvXL PCR1 4 RevXlinkChromatin K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001466 1466 GSM803352 Myers HudsonAlpha SL1397 PCR1x 4 input wgEncodeHaibTfbsK562RxlchPcr1xRawRep4 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control PCR1x ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchPcr1xRawRep3 K562 RvXL PCR1 3 RevXlinkChromatin K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001466 1466 GSM803352 Myers HudsonAlpha SL1396 PCR1x 3 input wgEncodeHaibTfbsK562RxlchPcr1xRawRep3 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control PCR1x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchPcr1xRawRep2 K562 RvXL PCR1 2 RevXlinkChromatin K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001466 1466 GSM803352 Myers HudsonAlpha SL519 PCR1x 2 input wgEncodeHaibTfbsK562RxlchPcr1xRawRep2 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562RxlchPcr1xRawRep1 K562 RvXL PCR1 1 RevXlinkChromatin K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001466 1466 GSM803352 Myers HudsonAlpha SL518 PCR1x 1 input wgEncodeHaibTfbsK562RxlchPcr1xRawRep1 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb7asc34508V0416101RawRep2 K562 ZBTB7A 2 ZBTB7A_(SC-34508) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001620 1620 GSM803473 Myers HudsonAlpha SL3183 v041610.1 2 exp wgEncodeHaibTfbsK562Zbtb7asc34508V0416101RawRep2 None RawSignal Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ZBTB7A v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb7asc34508V0416101RawRep1 K562 ZBTB7A 1 ZBTB7A_(SC-34508) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001620 1620 GSM803473 Myers HudsonAlpha SL2265 v041610.1 1 exp wgEncodeHaibTfbsK562Zbtb7asc34508V0416101RawRep1 None RawSignal Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ZBTB7A v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb33Pcr1xRawRep2 K562 ZBTB33 2 ZBTB33 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001569 1569 GSM803504 Myers HudsonAlpha SL1320 PCR1x 2 exp wgEncodeHaibTfbsK562Zbtb33Pcr1xRawRep2 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ZBTB33 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb33Pcr1xRawRep1 K562 ZBTB33 1 ZBTB33 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001569 1569 GSM803504 Myers HudsonAlpha SL1114 PCR1x 1 exp wgEncodeHaibTfbsK562Zbtb33Pcr1xRawRep1 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ZBTB33 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1sc281V0416101RawRep2 K562 YY1 V101 2 YY1_(SC-281) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEH001584 1584 GSM803446 Myers HudsonAlpha SL2944 v041610.1 2 exp wgEncodeHaibTfbsK562Yy1sc281V0416101RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1sc281V0416101RawRep1 K562 YY1 V101 1 YY1_(SC-281) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEH001584 1584 GSM803446 Myers HudsonAlpha SL2203 v041610.1 1 exp wgEncodeHaibTfbsK562Yy1sc281V0416101RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 YY1 281 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1V0416102RawRep2 K562 YY1 V102 2 YY1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001623 1623 GSM803470 Myers HudsonAlpha SL3071 v041610.2 2 exp wgEncodeHaibTfbsK562Yy1V0416102RawRep2 None RawSignal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 YY1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1V0416102RawRep1 K562 YY1 V102 1 YY1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001623 1623 GSM803470 Myers HudsonAlpha SL2946 v041610.2 1 exp wgEncodeHaibTfbsK562Yy1V0416102RawRep1 None RawSignal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 YY1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Usf1V0416101RawRep2 K562 USF1 V101 2 USF-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001583 1583 GSM803441 Myers HudsonAlpha SL3166 v041610.1 2 exp wgEncodeHaibTfbsK562Usf1V0416101RawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 USF-1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Usf1V0416101RawRep1 K562 USF1 V101 1 USF-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001583 1583 GSM803441 Myers HudsonAlpha SL3163 v041610.1 1 exp wgEncodeHaibTfbsK562Usf1V0416101RawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 USF-1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Trim28sc81411V0422111RawRep2 K562 TRIM28 V11 2 TRIM28_(SC-81411) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH003210 3210 GSM1010849 Myers HudsonAlpha SL9830 v042211.1 2 exp wgEncodeHaibTfbsK562Trim28sc81411V0422111RawRep2 None RawSignal The protein encoded by this gene mediates transcriptional control by interaction with the Kruppel-associated box repression domain found in many transcription factors. The protein localizes to the nucleus and is thought to associate with specific chromatin regions. The protein is a member of the tripartite motif family. This tripartite motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TRIM28 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Trim28sc81411V0422111RawRep1 K562 TRIM28 V11 1 TRIM28_(SC-81411) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH003210 3210 GSM1010849 Myers HudsonAlpha SL8672 v042211.1 1 exp wgEncodeHaibTfbsK562Trim28sc81411V0422111RawRep1 None RawSignal The protein encoded by this gene mediates transcriptional control by interaction with the Kruppel-associated box repression domain found in many transcription factors. The protein localizes to the nucleus and is thought to associate with specific chromatin regions. The protein is a member of the tripartite motif family. This tripartite motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TRIM28 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Thap1sc98174V0416101RawRep2 K562 THAP1 V101 2 THAP1_(SC-98174) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001655 1655 GSM803408 Myers HudsonAlpha SL3186 v041610.1 2 exp wgEncodeHaibTfbsK562Thap1sc98174V0416101RawRep2 None RawSignal The protein encoded by this gene contains a THAP domain, a conserved DNA-binding domain. This protein colocalizes with the apoptosis response protein PAWR/PAR-4 in promyelocytic leukemia (PML) nuclear bodies, and functions as a proapoptotic factor that links PAWR to PML nuclear bodies. Alternatively spliced transcript variants encoding distinct isoforms have been observed. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 THAP1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Thap1sc98174V0416101RawRep1 K562 THAP1 V101 1 THAP1_(SC-98174) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001655 1655 GSM803408 Myers HudsonAlpha SL2202 v041610.1 1 exp wgEncodeHaibTfbsK562Thap1sc98174V0416101RawRep1 None RawSignal The protein encoded by this gene contains a THAP domain, a conserved DNA-binding domain. This protein colocalizes with the apoptosis response protein PAWR/PAR-4 in promyelocytic leukemia (PML) nuclear bodies, and functions as a proapoptotic factor that links PAWR to PML nuclear bodies. Alternatively spliced transcript variants encoding distinct isoforms have been observed. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 THAP1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Tead4sc101184V0422111RawRep2 K562 TEAD4 V11 2 TEAD4_(SC-101184) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002333 2333 GSM1010895 Myers HudsonAlpha SL7841 v042211.1 2 exp wgEncodeHaibTfbsK562Tead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Tead4sc101184V0422111RawRep1 K562 TEAD4 V11 1 TEAD4_(SC-101184) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002333 2333 GSM1010895 Myers HudsonAlpha SL7571 v042211.1 1 exp wgEncodeHaibTfbsK562Tead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf7sc101167V0416101RawRep2 K562 TAF7 V101 2 TAF7_(SC-101167) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001654 1654 GSM803407 Myers HudsonAlpha SL3568 v041610.1 2 exp wgEncodeHaibTfbsK562Taf7sc101167V0416101RawRep2 None RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TAF7 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf7sc101167V0416101RawRep1 K562 TAF7 V101 1 TAF7_(SC-101167) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001654 1654 GSM803407 Myers HudsonAlpha SL3274 v041610.1 1 exp wgEncodeHaibTfbsK562Taf7sc101167V0416101RawRep1 None RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TAF7 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf1V0416101RawRep2 K562 TAF1 V101 2 TAF1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001582 1582 GSM803431 Myers HudsonAlpha SL2942 v041610.1 2 exp wgEncodeHaibTfbsK562Taf1V0416101RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TAF1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf1V0416101RawRep1 K562 TAF1 V101 1 TAF1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001582 1582 GSM803431 Myers HudsonAlpha SL2941 v041610.1 1 exp wgEncodeHaibTfbsK562Taf1V0416101RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 TAF1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Stat5asc74442V0422111RawRep2 K562 STAT5A V11 2 STAT5A_(SC-74442) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002347 2347 GSM1010877 Myers HudsonAlpha SL9116 v042211.1 2 exp wgEncodeHaibTfbsK562Stat5asc74442V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 STAT5A v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Stat5asc74442V0422111RawRep1 K562 STAT5A V11 1 STAT5A_(SC-74442) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002347 2347 GSM1010877 Myers HudsonAlpha SL8673 v042211.1 1 exp wgEncodeHaibTfbsK562Stat5asc74442V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 STAT5A v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562SrfV0416101RawRep2 K562 SRF V101 2 SRF K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001600 1600 GSM803520 Myers HudsonAlpha SL3272 v041610.1 2 exp wgEncodeHaibTfbsK562SrfV0416101RawRep2 None RawSignal Serum response transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SRF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562SrfV0416101RawRep1 K562 SRF V101 1 SRF K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001600 1600 GSM803520 Myers HudsonAlpha SL3162 v041610.1 1 exp wgEncodeHaibTfbsK562SrfV0416101RawRep1 None RawSignal Serum response transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SRF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp2sc643V0416102RawRep2 K562 SP2 V102 2 SP2_(SC-643) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001653 1653 GSM803402 Myers HudsonAlpha SL3361 v041610.2 2 exp wgEncodeHaibTfbsK562Sp2sc643V0416102RawRep2 None RawSignal This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SP2 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp2sc643V0416102RawRep1 K562 SP2 V102 1 SP2_(SC-643) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001653 1653 GSM803402 Myers HudsonAlpha SL2951 v041610.2 1 exp wgEncodeHaibTfbsK562Sp2sc643V0416102RawRep1 None RawSignal This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SP2 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp1Pcr1xRawRep2 K562 SP1 PCR1 2 SP1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001578 1578 GSM803505 Myers HudsonAlpha SL1510 PCR1x 2 exp wgEncodeHaibTfbsK562Sp1Pcr1xRawRep2 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SP1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp1Pcr1xRawRep1 K562 SP1 PCR1 1 SP1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001578 1578 GSM803505 Myers HudsonAlpha SL1197 PCR1x 1 exp wgEncodeHaibTfbsK562Sp1Pcr1xRawRep1 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SP1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5V0416101RawRep2 K562 SIX5 V101 2 SIX5 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001664 1664 GSM803378 Myers HudsonAlpha SL3990 v041610.1 2 exp wgEncodeHaibTfbsK562Six5V0416101RawRep2 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SIX5 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5V0416101RawRep1 K562 SIX5 V101 1 SIX5 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001664 1664 GSM803378 Myers HudsonAlpha SL3924 v041610.1 1 exp wgEncodeHaibTfbsK562Six5V0416101RawRep1 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SIX5 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5Pcr1xRawRep2 K562 SIX5 PCR1 2 SIX5 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001483 1483 GSM803383 Myers HudsonAlpha SL986 PCR1x 2 exp wgEncodeHaibTfbsK562Six5Pcr1xRawRep2 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SIX5 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5Pcr1xRawRep1 K562 SIX5 PCR1 1 SIX5 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001483 1483 GSM803383 Myers HudsonAlpha SL842 PCR1x 1 exp wgEncodeHaibTfbsK562Six5Pcr1xRawRep1 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 SIX5 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sin3ak20V0416101RawRep2 K562 Sin3A V101 2 Sin3Ak-20 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-03 2011-09-03 wgEncodeEH001607 1607 GSM803525 Myers HudsonAlpha SL3496 v041610.1 2 exp wgEncodeHaibTfbsK562Sin3ak20V0416101RawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sin3ak20V0416101RawRep1 K562 Sin3A V101 1 Sin3Ak-20 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-03 2011-09-03 wgEncodeEH001607 1607 GSM803525 Myers HudsonAlpha SL3273 v041610.1 1 exp wgEncodeHaibTfbsK562Sin3ak20V0416101RawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Sin3Ak-20 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Rad21V0416102RawRep2 K562 RAD21 V102 2 Rad21 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001585 1585 GSM803447 Myers HudsonAlpha SL3072 v041610.2 2 exp wgEncodeHaibTfbsK562Rad21V0416102RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 RAD21 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Rad21V0416102RawRep1 K562 RAD21 V102 1 Rad21 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001585 1585 GSM803447 Myers HudsonAlpha SL2947 v041610.2 1 exp wgEncodeHaibTfbsK562Rad21V0416102RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 RAD21 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pu1Pcr1xRawRep2 K562 PU.1 PCR1 2 PU.1 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001482 1482 GSM803384 Myers HudsonAlpha SL705 PCR1x 2 exp wgEncodeHaibTfbsK562Pu1Pcr1xRawRep2 None RawSignal PU.1 (H-135) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 PU.1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pu1Pcr1xRawRep1 K562 PU.1 PCR1 1 PU.1 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001482 1482 GSM803384 Myers HudsonAlpha SL646 PCR1x 1 exp wgEncodeHaibTfbsK562Pu1Pcr1xRawRep1 None RawSignal PU.1 (H-135) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 PU.1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol24h8V0416101RawRep2 K562 Pol2-4H8 V101 2 Pol2-4H8 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001581 1581 GSM803443 Myers HudsonAlpha SL2940 v041610.1 2 exp wgEncodeHaibTfbsK562Pol24h8V0416101RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol24h8V0416101RawRep1 K562 Pol2-4H8 V101 1 Pol2-4H8 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001581 1581 GSM803443 Myers HudsonAlpha SL2939 v041610.1 1 exp wgEncodeHaibTfbsK562Pol24h8V0416101RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Pol2-4H8 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol2V0416101RawRep2 K562 Pol2 V101 2 Pol2 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001633 1633 GSM803410 Myers HudsonAlpha SL3820 v041610.1 2 exp wgEncodeHaibTfbsK562Pol2V0416101RawRep2 None RawSignal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Pol2 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol2V0416101RawRep1 K562 Pol2 V101 1 Pol2 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001633 1633 GSM803410 Myers HudsonAlpha SL3819 v041610.1 1 exp wgEncodeHaibTfbsK562Pol2V0416101RawRep1 None RawSignal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Pol2 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pmlsc71910V0422111RawRep2 K562 PML V11 2 PML_(SC-71910) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002320 2320 GSM1010722 Myers HudsonAlpha SL8137 v042211.1 2 exp wgEncodeHaibTfbsK562Pmlsc71910V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 PML v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pmlsc71910V0422111RawRep1 K562 PML V11 1 PML_(SC-71910) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002320 2320 GSM1010722 Myers HudsonAlpha SL7894 v042211.1 1 exp wgEncodeHaibTfbsK562Pmlsc71910V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 PML v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562NrsfV0416102RawRep2 K562 NRSF V102 2 NRSF K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001638 1638 GSM803440 Myers HudsonAlpha SL3822 v041610.2 2 exp wgEncodeHaibTfbsK562NrsfV0416102RawRep2 None RawSignal Neuron-restrictive silencer transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 NRSF v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562NrsfV0416102RawRep1 K562 NRSF V102 1 NRSF K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001638 1638 GSM803440 Myers HudsonAlpha SL3821 v041610.2 1 exp wgEncodeHaibTfbsK562NrsfV0416102RawRep1 None RawSignal Neuron-restrictive silencer transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 NRSF v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Nr2f2sc271940V0422111RawRep2 K562 NR2F2 V11 2 NR2F2_(SC-271940) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002382 2382 GSM1010782 Myers HudsonAlpha SL8577 v042211.1 2 exp wgEncodeHaibTfbsK562Nr2f2sc271940V0422111RawRep2 None RawSignal This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 NR2F2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Nr2f2sc271940V0422111RawRep1 K562 NR2F2 V11 1 NR2F2_(SC-271940) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002382 2382 GSM1010782 Myers HudsonAlpha SL8143 v042211.1 1 exp wgEncodeHaibTfbsK562Nr2f2sc271940V0422111RawRep1 None RawSignal This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 NR2F2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Mef2aV0416101RawRep2 K562 MEF2A V101 2 MEF2A K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001663 1663 GSM803379 Myers HudsonAlpha SL3925 v041610.1 2 exp wgEncodeHaibTfbsK562Mef2aV0416101RawRep2 None RawSignal The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 MEF2A v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Mef2aV0416101RawRep1 K562 MEF2A V101 1 MEF2A K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001663 1663 GSM803379 Myers HudsonAlpha SL1794 v041610.1 1 exp wgEncodeHaibTfbsK562Mef2aV0416101RawRep1 None RawSignal The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 MEF2A v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562MaxV0416102RawRep2 K562 Max V102 2 Max K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001605 1605 GSM803523 Myers HudsonAlpha SL3070 v041610.2 2 exp wgEncodeHaibTfbsK562MaxV0416102RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Max v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562MaxV0416102RawRep1 K562 Max V102 1 Max K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001605 1605 GSM803523 Myers HudsonAlpha SL2945 v041610.2 1 exp wgEncodeHaibTfbsK562MaxV0416102RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Max v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Hdac2sc6296V0416102RawRep2 K562 HDAC2 V102 2 HDAC2_(SC-6296) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001622 1622 GSM803471 Myers HudsonAlpha SL3359 v041610.2 2 exp wgEncodeHaibTfbsK562Hdac2sc6296V0416102RawRep2 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 HDAC2 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Hdac2sc6296V0416102RawRep1 K562 HDAC2 V102 1 HDAC2_(SC-6296) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001622 1622 GSM803471 Myers HudsonAlpha SL2952 v041610.2 1 exp wgEncodeHaibTfbsK562Hdac2sc6296V0416102RawRep1 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 HDAC2 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Gata2sc267Pcr1xRawRep2 K562 GATA2 PCR1 2 GATA2_(SC-267) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001576 1576 GSM803540 Myers HudsonAlpha SL1665 PCR1x 2 exp wgEncodeHaibTfbsK562Gata2sc267Pcr1xRawRep2 None RawSignal This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded program plays an essential role in regulation transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 GATA2 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Gata2sc267Pcr1xRawRep1 K562 GATA2 PCR1 1 GATA2_(SC-267) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001576 1576 GSM803540 Myers HudsonAlpha SL1430 PCR1x 1 exp wgEncodeHaibTfbsK562Gata2sc267Pcr1xRawRep1 None RawSignal This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded program plays an essential role in regulation transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 GATA2 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562GabpV0416101RawRep2 K562 GABP V101 2 GABP K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001604 1604 GSM803524 Myers HudsonAlpha SL3356 v041610.1 2 exp wgEncodeHaibTfbsK562GabpV0416101RawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 GABP v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562GabpV0416101RawRep1 K562 GABP V101 1 GABP K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001604 1604 GSM803524 Myers HudsonAlpha SL2943 v041610.1 1 exp wgEncodeHaibTfbsK562GabpV0416101RawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 GABP v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep2 K562 FOSL1 V101 2 FOSL1_(SC-183) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001637 1637 GSM803439 Myers HudsonAlpha SL3187 v041610.1 2 exp wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep2 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 FOSL1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep1 K562 FOSL1 V101 1 FOSL1_(SC-183) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001637 1637 GSM803439 Myers HudsonAlpha SL2349 v041610.1 1 exp wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep1 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 FOSL1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ets1V0416101RawRep2 K562 ETS1 V101 2 ETS1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001580 1580 GSM803442 Myers HudsonAlpha SL3182 v041610.1 2 exp wgEncodeHaibTfbsK562Ets1V0416101RawRep2 None RawSignal ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ETS1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ets1V0416101RawRep1 K562 ETS1 V101 1 ETS1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001580 1580 GSM803442 Myers HudsonAlpha SL2262 v041610.1 1 exp wgEncodeHaibTfbsK562Ets1V0416101RawRep1 None RawSignal ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ETS1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Elf1sc631V0416102RawRep2 K562 ELF1 V102 2 ELF1_(SC-631) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001619 1619 GSM803494 Myers HudsonAlpha SL3360 v041610.2 2 exp wgEncodeHaibTfbsK562Elf1sc631V0416102RawRep2 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ELF1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Elf1sc631V0416102RawRep1 K562 ELF1 V102 1 ELF1_(SC-631) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001619 1619 GSM803494 Myers HudsonAlpha SL2950 v041610.2 1 exp wgEncodeHaibTfbsK562Elf1sc631V0416102RawRep1 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ELF1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Egr1V0416101RawRep2 K562 Egr-1 V101 2 Egr-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001646 1646 GSM803414 Myers HudsonAlpha SL3497 v041610.1 2 exp wgEncodeHaibTfbsK562Egr1V0416101RawRep2 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Egr-1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Egr1V0416101RawRep1 K562 Egr-1 V101 1 Egr-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001646 1646 GSM803414 Myers HudsonAlpha SL3164 v041610.1 1 exp wgEncodeHaibTfbsK562Egr1V0416101RawRep1 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Egr-1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562E2f6V0416102RawRep2 K562 E2F6 V102 2 E2F6 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001598 1598 GSM803469 Myers HudsonAlpha SL3073 v041610.2 2 exp wgEncodeHaibTfbsK562E2f6V0416102RawRep2 None RawSignal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 E2F6 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562E2f6V0416102RawRep1 K562 E2F6 V102 1 E2F6 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001598 1598 GSM803469 Myers HudsonAlpha SL2948 v041610.2 1 exp wgEncodeHaibTfbsK562E2f6V0416102RawRep1 None RawSignal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 E2F6 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562CtcfcPcr1xRawRep2 K562 CTCF PCR1 2 CTCF_(SC-5916) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002279 2279 GSM1010820 Myers HudsonAlpha SL5605 PCR1x 2 exp wgEncodeHaibTfbsK562CtcfcPcr1xRawRep2 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CTCF 5916 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562CtcfcPcr1xRawRep1V2 K562 CTCF PCR1 1 CTCF_(SC-5916) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-21 wgEncodeEH002279 2279 GSM1010820 Myers HudsonAlpha SL3075 PCR1x 1 exp wgEncodeHaibTfbsK562CtcfcPcr1xRawRep1V2 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CTCF 5916 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ctcflsc98982V0416101RawRep2 K562 CTCFL V101 2 CTCFL_(SC-98982) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001652 1652 GSM803401 Myers HudsonAlpha SL3972 v041610.1 2 exp wgEncodeHaibTfbsK562Ctcflsc98982V0416101RawRep2 None RawSignal CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily in the nucleus of somatic cells. CTCF and the protein encoded by this gene are normally expressed in a mutually exclusive pattern that correlates with resetting of methylation marks during male germ cell differentiation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CTCFL v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ctcflsc98982V0416101RawRep1 K562 CTCFL V101 1 CTCFL_(SC-98982) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001652 1652 GSM803401 Myers HudsonAlpha SL3189 v041610.1 1 exp wgEncodeHaibTfbsK562Ctcflsc98982V0416101RawRep1 None RawSignal CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily in the nucleus of somatic cells. CTCF and the protein encoded by this gene are normally expressed in a mutually exclusive pattern that correlates with resetting of methylation marks during male germ cell differentiation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CTCFL v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Creb1sc240V0422111RawRep2 K562 CREB1 V11 2 CREB1_(SC-240) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003230 3230 GSM1010890 Myers HudsonAlpha SL13293 v042211.1 2 exp wgEncodeHaibTfbsK562Creb1sc240V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CREB1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Creb1sc240V0422111RawRep1 K562 CREB1 V11 1 CREB1_(SC-240) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003230 3230 GSM1010890 Myers HudsonAlpha SL12420 v042211.1 1 exp wgEncodeHaibTfbsK562Creb1sc240V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CREB1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cebpdsc636V0422111RawRep2 K562 CEBPD V11 2 CEBPD_(SC-636) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEH003432 3432 GSM1010906 Myers HudsonAlpha SL13317 v042211.1 2 exp wgEncodeHaibTfbsK562Cebpdsc636V0422111RawRep2 None RawSignal The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CEBPD v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIBd Regulation 
wgEncodeHaibTfbsK562Cebpdsc636V0422111RawRep1 K562 CEBPD V11 1 CEBPD_(SC-636) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEH003432 3432 GSM1010906 Myers HudsonAlpha SL11280 v042211.1 1 exp wgEncodeHaibTfbsK562Cebpdsc636V0422111RawRep1 None RawSignal The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CEBPD v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIBd Regulation 
wgEncodeHaibTfbsK562Cebpbsc150V0422111RawRep2 K562 CEBPB V11 2 CEBPB_(SC-150) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002346 2346 GSM1010878 Myers HudsonAlpha SL9547 v042211.1 2 exp wgEncodeHaibTfbsK562Cebpbsc150V0422111RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CEBPB v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cebpbsc150V0422111RawRep1 K562 CEBPB V11 1 CEBPB_(SC-150) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002346 2346 GSM1010878 Myers HudsonAlpha SL8085 v042211.1 1 exp wgEncodeHaibTfbsK562Cebpbsc150V0422111RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CEBPB v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cbx3sc101004V0422111RawRep2 K562 CBX3 V11 2 CBX3_(SC-101004) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002383 2383 GSM1010732 Myers HudsonAlpha SL7568 v042211.1 2 exp wgEncodeHaibTfbsK562Cbx3sc101004V0422111RawRep2 None RawSignal At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CBX3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cbx3sc101004V0422111RawRep1 K562 CBX3 V11 1 CBX3_(SC-101004) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002383 2383 GSM1010732 Myers HudsonAlpha SL7105 v042211.1 1 exp wgEncodeHaibTfbsK562Cbx3sc101004V0422111RawRep1 None RawSignal At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CBX3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Bclaf101388Pcr1xRawRep2 K562 BCLAF1 2 BCLAF1_(SC-101388) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001571 1571 GSM803515 Myers HudsonAlpha SL1512 PCR1x 2 exp wgEncodeHaibTfbsK562Bclaf101388Pcr1xRawRep2 None RawSignal This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 BCLAF1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Bclaf101388Pcr1xRawRep1 K562 BCLAF1 1 BCLAF1_(SC-101388) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001571 1571 GSM803515 Myers HudsonAlpha SL1273 PCR1x 1 exp wgEncodeHaibTfbsK562Bclaf101388Pcr1xRawRep1 None RawSignal This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 BCLAF1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Atf3V0416101RawRep2 K562 ATF3 V101 2 ATF3 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001662 1662 GSM803380 Myers HudsonAlpha SL3926 v041610.1 2 exp wgEncodeHaibTfbsK562Atf3V0416101RawRep2 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ATF3 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Atf3V0416101RawRep1 K562 ATF3 V101 1 ATF3 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001662 1662 GSM803380 Myers HudsonAlpha SL3184 v041610.1 1 exp wgEncodeHaibTfbsK562Atf3V0416101RawRep1 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 ATF3 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxlchV0422111RawRep2 hESC RvXL V11 2 RevXlinkChromatin H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH002276 2276 GSM1010815 Myers HudsonAlpha SL12796 v042211.1 2 input wgEncodeHaibTfbsH1hescRxlchV0422111RawRep2 None RawSignal embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Control v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxlchV0422111RawRep1 hESC RvXL V11 1 RevXlinkChromatin H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-07-18 2012-04-18 wgEncodeEH002276 2276 GSM1010815 Myers HudsonAlpha SL6018 v042211.1 1 input wgEncodeHaibTfbsH1hescRxlchV0422111RawRep1 None RawSignal embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxlchV0416102RawRep1 hESC RvXL V102 1 RevXlinkChromatin H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001497 1497 GSM803364 Myers HudsonAlpha SL969 v041610.2 1 input wgEncodeHaibTfbsH1hescRxlchV0416102RawRep1 None RawSignal embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Control v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxlchPcr1xRawRep1 hESC RvXL PCR1 1 RevXlinkChromatin H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001543 1543 GSM803339 Myers HudsonAlpha SL1398 PCR1x 1 input wgEncodeHaibTfbsH1hescRxlchPcr1xRawRep1 None RawSignal embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescYy1sc281V0416102RawRep2 hESC YY1 V102 2 YY1_(SC-281) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001567 1567 GSM803513 Myers HudsonAlpha SL1967 v041610.2 2 exp wgEncodeHaibTfbsH1hescYy1sc281V0416102RawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC YY1 281 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescYy1sc281V0416102RawRep1 hESC YY1 V102 1 YY1_(SC-281) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001567 1567 GSM803513 Myers HudsonAlpha SL1657 v041610.2 1 exp wgEncodeHaibTfbsH1hescYy1sc281V0416102RawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC YY1 281 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescUsf1Pcr1xRawRep2 hESC USF1 PCR1 2 USF-1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001532 1532 GSM803426 Myers HudsonAlpha SL1319 PCR1x 2 exp wgEncodeHaibTfbsH1hescUsf1Pcr1xRawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC USF-1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescUsf1Pcr1xRawRep1 hESC USF1 PCR1 1 USF-1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001532 1532 GSM803426 Myers HudsonAlpha SL1159 PCR1x 1 exp wgEncodeHaibTfbsH1hescUsf1Pcr1xRawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC USF-1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTead4sc101184V0422111RawRep2 hESC TEAD4 V11 2 TEAD4_(SC-101184) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003214 3214 GSM1010845 Myers HudsonAlpha SL12417 v042211.1 2 exp wgEncodeHaibTfbsH1hescTead4sc101184V0422111RawRep2 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TEAD4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTead4sc101184V0422111RawRep1 hESC TEAD4 V11 1 TEAD4_(SC-101184) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003214 3214 GSM1010845 Myers HudsonAlpha SL10882 v042211.1 1 exp wgEncodeHaibTfbsH1hescTead4sc101184V0422111RawRep1 None RawSignal Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TEAD4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTcf12Pcr1xRawRep2 hESC TCF12 PCR1 2 TCF12 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001531 1531 GSM803427 Myers HudsonAlpha SL1315 PCR1x 2 exp wgEncodeHaibTfbsH1hescTcf12Pcr1xRawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TCF12 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTcf12Pcr1xRawRep1 hESC TCF12 PCR1 1 TCF12 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001531 1531 GSM803427 Myers HudsonAlpha SL1158 PCR1x 1 exp wgEncodeHaibTfbsH1hescTcf12Pcr1xRawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TCF12 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf7sc101167V0416102RawRep2 hESC TAF7 V102 2 TAF7_(SC-101167) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-13 2011-09-13 wgEncodeEH001610 1610 GSM803501 Myers HudsonAlpha SL3062 v041610.2 2 exp wgEncodeHaibTfbsH1hescTaf7sc101167V0416102RawRep2 None RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TAF7 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf7sc101167V0416102RawRep1 hESC TAF7 V102 1 TAF7_(SC-101167) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-13 2011-09-13 wgEncodeEH001610 1610 GSM803501 Myers HudsonAlpha SL2697 v041610.2 1 exp wgEncodeHaibTfbsH1hescTaf7sc101167V0416102RawRep1 None RawSignal The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TAF7 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf1V0416102RawRep2 hESC TAF1 V102 2 TAF1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001500 1500 GSM803450 Myers HudsonAlpha SL964 v041610.2 2 exp wgEncodeHaibTfbsH1hescTaf1V0416102RawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TAF1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf1V0416102RawRep1 hESC TAF1 V102 1 TAF1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001500 1500 GSM803450 Myers HudsonAlpha SL853 v041610.2 1 exp wgEncodeHaibTfbsH1hescTaf1V0416102RawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC TAF1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSrfPcr1xRawRep2 hESC SRF PCR1 2 SRF H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001533 1533 GSM803425 Myers HudsonAlpha SL1659 PCR1x 2 exp wgEncodeHaibTfbsH1hescSrfPcr1xRawRep2 None RawSignal Serum response transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SRF PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSrfPcr1xRawRep1 hESC SRF PCR1 1 SRF H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001533 1533 GSM803425 Myers HudsonAlpha SL1483 PCR1x 1 exp wgEncodeHaibTfbsH1hescSrfPcr1xRawRep1 None RawSignal Serum response transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SRF PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp4v20V0422111RawRep2 hESC SP4 V11 2 SP4_(V-20) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002317 2317 GSM1010743 Myers HudsonAlpha SL8135 v042211.1 2 exp wgEncodeHaibTfbsH1hescSp4v20V0422111RawRep2 None RawSignal Binds to GT and GC boxes promoters elements. Probable transcriptional activator. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SP4 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp4v20V0422111RawRep1 hESC SP4 V11 1 SP4_(V-20) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002317 2317 GSM1010743 Myers HudsonAlpha SL7836 v042211.1 1 exp wgEncodeHaibTfbsH1hescSp4v20V0422111RawRep1 None RawSignal Binds to GT and GC boxes promoters elements. Probable transcriptional activator. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SP4 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp2V0422111RawRep2 hESC SP2 V11 2 SP2_(SC-643) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-07 2012-06-07 wgEncodeEH002302 2302 GSM1010776 Myers HudsonAlpha SL6005 v042211.1 2 exp wgEncodeHaibTfbsH1hescSp2V0422111RawRep2 None RawSignal This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SP2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp2V0422111RawRep1 hESC SP2 V11 1 SP2_(SC-643) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-07 2012-06-07 wgEncodeEH002302 2302 GSM1010776 Myers HudsonAlpha SL5690 v042211.1 1 exp wgEncodeHaibTfbsH1hescSp2V0422111RawRep1 None RawSignal This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SP2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp1Pcr1xRawRep2 hESC SP1 PCR1 2 SP1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001529 1529 GSM803377 Myers HudsonAlpha SL1318 PCR1x 2 exp wgEncodeHaibTfbsH1hescSp1Pcr1xRawRep2 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SP1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp1Pcr1xRawRep1 hESC SP1 PCR1 1 SP1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001529 1529 GSM803377 Myers HudsonAlpha SL1166 PCR1x 1 exp wgEncodeHaibTfbsH1hescSp1Pcr1xRawRep1 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SP1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSix5Pcr1xRawRep2 hESC SIX5 PCR1 2 SIX5 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001528 1528 GSM803405 Myers HudsonAlpha SL1317 PCR1x 2 exp wgEncodeHaibTfbsH1hescSix5Pcr1xRawRep2 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SIX5 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSix5Pcr1xRawRep1 hESC SIX5 PCR1 1 SIX5 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001528 1528 GSM803405 Myers HudsonAlpha SL1162 PCR1x 1 exp wgEncodeHaibTfbsH1hescSix5Pcr1xRawRep1 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC SIX5 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSin3ak20Pcr1xRawRep2 hESC Sin3A PCR1 2 Sin3Ak-20 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001530 1530 GSM803428 Myers HudsonAlpha SL1313 PCR1x 2 exp wgEncodeHaibTfbsH1hescSin3ak20Pcr1xRawRep2 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Sin3Ak-20 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSin3ak20Pcr1xRawRep1 hESC Sin3A PCR1 1 Sin3Ak-20 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001530 1530 GSM803428 Myers HudsonAlpha SL1157 PCR1x 1 exp wgEncodeHaibTfbsH1hescSin3ak20Pcr1xRawRep1 None RawSignal Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Sin3Ak-20 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxraV0416102RawRep2 hESC RXRA V102 2 RXRA H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001560 1560 GSM803506 Myers HudsonAlpha SL2346 v041610.2 2 exp wgEncodeHaibTfbsH1hescRxraV0416102RawRep2 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC RXRA v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxraV0416102RawRep1 hESC RXRA V102 1 RXRA H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-11-29 2011-08-28 wgEncodeEH001560 1560 GSM803506 Myers HudsonAlpha SL1163 v041610.2 1 exp wgEncodeHaibTfbsH1hescRxraV0416102RawRep1 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC RXRA v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRad21V0416102RawRep2 hESC RAD21 V102 2 Rad21 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001593 1593 GSM803466 Myers HudsonAlpha SL3066 v041610.2 2 exp wgEncodeHaibTfbsH1hescRad21V0416102RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC RAD21 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRad21V0416102RawRep1 hESC RAD21 V102 1 Rad21 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001593 1593 GSM803466 Myers HudsonAlpha SL2689 v041610.2 1 exp wgEncodeHaibTfbsH1hescRad21V0416102RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC RAD21 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102RawRep2 hESC POU5F1 2 POU5F1_(SC-9081) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001636 1636 GSM803438 Myers HudsonAlpha SL3453 v041610.2 2 exp wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102RawRep2 None RawSignal This gene encodes a transcription factor containing a POU homeodomain. This transcription factor plays a role in embryonic development, especially during early embryogenesis, and it is necessary for embryonic stem cell pluripotency. A translocation of this gene with the Ewing's sarcoma gene, t(6;22)(p21;q12), has been linked to tumor formation. Alternative splicing, as well as usage of alternative translation initiation codons, results in multiple isoforms, one of which initiates at a non-AUG (CUG) start codon. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12 (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC POU5F1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102RawRep1 hESC POU5F1 1 POU5F1_(SC-9081) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001636 1636 GSM803438 Myers HudsonAlpha SL2548 v041610.2 1 exp wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102RawRep1 None RawSignal This gene encodes a transcription factor containing a POU homeodomain. This transcription factor plays a role in embryonic development, especially during early embryogenesis, and it is necessary for embryonic stem cell pluripotency. A translocation of this gene with the Ewing's sarcoma gene, t(6;22)(p21;q12), has been linked to tumor formation. Alternative splicing, as well as usage of alternative translation initiation codons, results in multiple isoforms, one of which initiates at a non-AUG (CUG) start codon. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12 (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC POU5F1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol24h8V0416102RawRep2 hESC Pol2-4H8 V102 2 Pol2-4H8 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001514 1514 GSM803484 Myers HudsonAlpha SL1051 v041610.2 2 exp wgEncodeHaibTfbsH1hescPol24h8V0416102RawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Pol2-4H8 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol24h8V0416102RawRep1 hESC Pol2-4H8 V102 1 Pol2-4H8 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001514 1514 GSM803484 Myers HudsonAlpha SL979 v041610.2 1 exp wgEncodeHaibTfbsH1hescPol24h8V0416102RawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Pol2-4H8 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol2V0416102RawRep2 hESC Pol2 V102 2 Pol2 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001499 1499 GSM803366 Myers HudsonAlpha SL1052 v041610.2 2 exp wgEncodeHaibTfbsH1hescPol2V0416102RawRep2 None RawSignal RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Pol2 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol2V0416102RawRep1 hESC Pol2 V102 1 Pol2 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001499 1499 GSM803366 Myers HudsonAlpha SL980 v041610.2 1 exp wgEncodeHaibTfbsH1hescPol2V0416102RawRep1 None RawSignal RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Pol2 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescP300V0416102RawRep2 hESC p300 V102 2 p300 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001574 1574 GSM803542 Myers HudsonAlpha SL1883 v041610.2 2 exp wgEncodeHaibTfbsH1hescP300V0416102RawRep2 None RawSignal EP300(c-20) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC p300 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescP300V0416102RawRep1 hESC p300 V102 1 p300 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001574 1574 GSM803542 Myers HudsonAlpha SL2250 v041610.2 1 exp wgEncodeHaibTfbsH1hescP300V0416102RawRep1 None RawSignal EP300(c-20) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC p300 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNrsfV0416102RawRep2 hESC NRSF V102 2 NRSF H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001498 1498 GSM803365 Myers HudsonAlpha SL1053 v041610.2 2 exp wgEncodeHaibTfbsH1hescNrsfV0416102RawRep2 None RawSignal Neuron-restrictive silencer transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC NRSF v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNrsfV0416102RawRep1 hESC NRSF V102 1 NRSF H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001498 1498 GSM803365 Myers HudsonAlpha SL978 v041610.2 1 exp wgEncodeHaibTfbsH1hescNrsfV0416102RawRep1 None RawSignal Neuron-restrictive silencer transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC NRSF v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNanogsc33759V0416102RawRep2 hESC NANOG V102 2 NANOG_(SC-33759) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001635 1635 GSM803437 Myers HudsonAlpha SL3068 v041610.2 2 exp wgEncodeHaibTfbsH1hescNanogsc33759V0416102RawRep2 None RawSignal Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes (By similarity). Acts as a transcriptional activator or repressor (By similarity). Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3' (By similarity). When overexpressed, promotes cells to enter into S phase and proliferation (By similarity) (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC NANOG v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNanogsc33759V0416102RawRep1 hESC NANOG V102 1 NANOG_(SC-33759) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001635 1635 GSM803437 Myers HudsonAlpha SL2687 v041610.2 1 exp wgEncodeHaibTfbsH1hescNanogsc33759V0416102RawRep1 None RawSignal Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes (By similarity). Acts as a transcriptional activator or repressor (By similarity). Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3' (By similarity). When overexpressed, promotes cells to enter into S phase and proliferation (By similarity) (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC NANOG v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescMaxV0422111RawRep2 hESC Max V11 2 Max H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003225 3225 GSM1010898 Myers HudsonAlpha SL13302 v042211.1 2 exp wgEncodeHaibTfbsH1hescMaxV0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Max v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescMaxV0422111RawRep1 hESC Max V11 1 Max H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003225 3225 GSM1010898 Myers HudsonAlpha SL12411 v042211.1 1 exp wgEncodeHaibTfbsH1hescMaxV0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Max v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescJundV0416102RawRep2 hESC JunD V102 2 JunD H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001579 1579 GSM803529 Myers HudsonAlpha SL3065 v041610.2 2 exp wgEncodeHaibTfbsH1hescJundV0416102RawRep2 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC JunD v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescJundV0416102RawRep1 hESC JunD V102 1 JunD H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001579 1579 GSM803529 Myers HudsonAlpha SL2690 v041610.2 1 exp wgEncodeHaibTfbsH1hescJundV0416102RawRep1 None RawSignal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC JunD v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescHdac2sc6296V0416102RawRep2 hESC HDAC2 V102 2 HDAC2_(SC-6296) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2011-12-02 wgEncodeEH001659 1659 GSM803345 Myers HudsonAlpha SL3454 v041610.2 2 exp wgEncodeHaibTfbsH1hescHdac2sc6296V0416102RawRep2 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC HDAC2 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescHdac2sc6296V0416102RawRep1 hESC HDAC2 V102 1 HDAC2_(SC-6296) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2011-12-02 wgEncodeEH001659 1659 GSM803345 Myers HudsonAlpha SL3935 v041610.2 1 exp wgEncodeHaibTfbsH1hescHdac2sc6296V0416102RawRep1 None RawSignal This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC HDAC2 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescGabpPcr1xRawRep2 hESC GABP PCR1 2 GABP H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001534 1534 GSM803424 Myers HudsonAlpha SL1660 PCR1x 2 exp wgEncodeHaibTfbsH1hescGabpPcr1xRawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC GABP PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescGabpPcr1xRawRep1 hESC GABP PCR1 1 GABP H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001534 1534 GSM803424 Myers HudsonAlpha SL1518 PCR1x 1 exp wgEncodeHaibTfbsH1hescGabpPcr1xRawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC GABP PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescFosl1sc183V0416102RawRep2 hESC FOSL1 V102 2 FOSL1_(SC-183) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001660 1660 GSM803382 Myers HudsonAlpha SL4211 v041610.2 2 exp wgEncodeHaibTfbsH1hescFosl1sc183V0416102RawRep2 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC FOSL1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescFosl1sc183V0416102RawRep1 hESC FOSL1 V102 1 FOSL1_(SC-183) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001660 1660 GSM803382 Myers HudsonAlpha SL2692 v041610.2 1 exp wgEncodeHaibTfbsH1hescFosl1sc183V0416102RawRep1 None RawSignal The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC FOSL1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescEgr1V0416102RawRep2 hESC Egr-1 V102 2 Egr-1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001538 1538 GSM803430 Myers HudsonAlpha SL1885 v041610.2 2 exp wgEncodeHaibTfbsH1hescEgr1V0416102RawRep2 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Egr-1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescEgr1V0416102RawRep1 hESC Egr-1 V102 1 Egr-1 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001538 1538 GSM803430 Myers HudsonAlpha SL1482 v041610.2 1 exp wgEncodeHaibTfbsH1hescEgr1V0416102RawRep1 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC Egr-1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescE2f6V0422111RawRep2 hESC E2F6 V11 2 E2F6 H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003224 3224 GSM1010899 Myers HudsonAlpha SL13304 v042211.1 2 exp wgEncodeHaibTfbsH1hescE2f6V0422111RawRep2 None RawSignal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC E2F6 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescE2f6V0422111RawRep1 hESC E2F6 V11 1 E2F6 H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003224 3224 GSM1010899 Myers HudsonAlpha SL12414 v042211.1 1 exp wgEncodeHaibTfbsH1hescE2f6V0422111RawRep1 None RawSignal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC E2F6 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCtcfsc5916V0416102RawRep2 hESC CTCF V102 2 CTCF_(SC-5916) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001649 1649 GSM803419 Myers HudsonAlpha SL3067 v041610.2 2 exp wgEncodeHaibTfbsH1hescCtcfsc5916V0416102RawRep2 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC CTCF 5916 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCtcfsc5916V0416102RawRep1 hESC CTCF V102 1 CTCF_(SC-5916) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001649 1649 GSM803419 Myers HudsonAlpha SL2688 v041610.2 1 exp wgEncodeHaibTfbsH1hescCtcfsc5916V0416102RawRep1 None RawSignal This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC CTCF 5916 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCreb1sc240V0422111RawRep2 hESC CREB1 V11 2 CREB1_(SC-240) H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003229 3229 GSM1010896 Myers HudsonAlpha SL13303 v042211.1 2 exp wgEncodeHaibTfbsH1hescCreb1sc240V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC CREB1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCreb1sc240V0422111RawRep1 hESC CREB1 V11 1 CREB1_(SC-240) H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003229 3229 GSM1010896 Myers HudsonAlpha SL12413 v042211.1 1 exp wgEncodeHaibTfbsH1hescCreb1sc240V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC CREB1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescBcl11aV0416102RawRep2 hESC BCL V102 2 BCL11A H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001625 1625 GSM803476 Myers HudsonAlpha SL3989 v041610.2 2 exp wgEncodeHaibTfbsH1hescBcl11aV0416102RawRep2 None RawSignal This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC BCL11A v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescBcl11aPcr1xRawRep1 hESC BCL11A 1 BCL11A H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001527 1527 GSM803396 Myers HudsonAlpha SL1314 PCR1x 1 exp wgEncodeHaibTfbsH1hescBcl11aPcr1xRawRep1 None RawSignal This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC BCL11A PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf3V0416102RawRep2 hESC ATF3 V102 2 ATF3 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001566 1566 GSM803512 Myers HudsonAlpha SL1968 v041610.2 2 exp wgEncodeHaibTfbsH1hescAtf3V0416102RawRep2 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC ATF3 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf3V0416102RawRep1 hESC ATF3 V102 1 ATF3 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001566 1566 GSM803512 Myers HudsonAlpha SL1519 v041610.2 1 exp wgEncodeHaibTfbsH1hescAtf3V0416102RawRep1 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC ATF3 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf2sc81188V0422111RawRep2 hESC ATF2 V11 2 ATF2_(SC-81188) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002316 2316 GSM1010742 Myers HudsonAlpha SL8136 v042211.1 2 exp wgEncodeHaibTfbsH1hescAtf2sc81188V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC ATF2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf2sc81188V0422111RawRep1 hESC ATF2 V11 1 ATF2_(SC-81188) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002316 2316 GSM1010742 Myers HudsonAlpha SL7904 v042211.1 1 exp wgEncodeHaibTfbsH1hescAtf2sc81188V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) H1-hESC ATF2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchV0422111RawRep4 GM78 RvXL V11 4 RevXlinkChromatin GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003422 3422 GSM1010867 Myers HudsonAlpha SL12789 v042211.1 4 input wgEncodeHaibTfbsGm12878RxlchV0422111RawRep4 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control v042211.1 ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchV0422111RawRep3 GM78 RvXL V11 3 RevXlinkChromatin GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003422 3422 GSM1010867 Myers HudsonAlpha SL12049 v042211.1 3 input wgEncodeHaibTfbsGm12878RxlchV0422111RawRep3 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control v042211.1 ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchV0422111RawRep1 GM78 RvXL V11 1 RevXlinkChromatin GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH003422 3422 GSM1010867 Myers HudsonAlpha SL6022 v042211.1 1 input wgEncodeHaibTfbsGm12878RxlchV0422111RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchV0416102RawRep1 GM78 RvXL V102 1 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001647 1647 GSM803413 Myers HudsonAlpha SL3979 v041610.2 1 input wgEncodeHaibTfbsGm12878RxlchV0416102RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchV0416101RawRep1 GM78 RvXL V101 1 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001634 1634 GSM803436 Myers HudsonAlpha SL1613 v041610.1 1 input wgEncodeHaibTfbsGm12878RxlchV0416101RawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr2xRawRep2 GM78 RvXL PCR2 2 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001469 1469 GSM803346 Myers HudsonAlpha SL218 PCR2x 2 input wgEncodeHaibTfbsGm12878RxlchPcr2xRawRep2 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr2xRawRep1 GM78 RvXL PCR2 1 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001469 1469 GSM803346 Myers HudsonAlpha SL217 PCR2x 1 input wgEncodeHaibTfbsGm12878RxlchPcr2xRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep5 GM78 RvXL PCR1 5 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001467 1467 GSM803351 Myers HudsonAlpha SL1395 PCR1x 5 input wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep5 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR1x ChIP-seq Raw Signal Rep 5 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep4 GM78 RvXL PCR1 4 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001467 1467 GSM803351 Myers HudsonAlpha SL1394 PCR1x 4 input wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep4 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR1x ChIP-seq Raw Signal Rep 4 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep3 GM78 RvXL PCR1 3 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001467 1467 GSM803351 Myers HudsonAlpha SL678 PCR1x 3 input wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep3 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR1x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep2 GM78 RvXL PCR1 2 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001467 1467 GSM803351 Myers HudsonAlpha SL517 PCR1x 2 input wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep2 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep1 GM78 RvXL PCR1 1 RevXlinkChromatin GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001467 1467 GSM803351 Myers HudsonAlpha SL516 PCR1x 1 input wgEncodeHaibTfbsGm12878RxlchPcr1xRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Control PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102RawRep2 GM78 ZEB1 V102 2 ZEB1_(SC-25388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001645 1645 GSM803411 Myers HudsonAlpha SL3254 v041610.2 2 exp wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102RawRep2 None RawSignal This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ZEB1 v041610.2 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102RawRep1 GM78 ZEB1 V102 1 ZEB1_(SC-25388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001645 1645 GSM803411 Myers HudsonAlpha SL2957 v041610.2 1 exp wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102RawRep1 None RawSignal This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ZEB1 v041610.2 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zbtb33Pcr1xRawRep2 GM78 ZBTB33 2 ZBTB33 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001488 1488 GSM803392 Myers HudsonAlpha SL923 PCR1x 2 exp wgEncodeHaibTfbsGm12878Zbtb33Pcr1xRawRep2 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ZBTB33 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zbtb33Pcr1xRawRep1 GM78 ZBTB33 1 ZBTB33 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001488 1488 GSM803392 Myers HudsonAlpha SL814 PCR1x 1 exp wgEncodeHaibTfbsGm12878Zbtb33Pcr1xRawRep1 None RawSignal KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ZBTB33 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xRawRep2 GM78 YY1 PCR1 2 YY1_(SC-281) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-15 2011-11-15 wgEncodeEH001657 1657 GSM803406 Myers HudsonAlpha SL2129 PCR1x 2 exp wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xRawRep2 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 YY1 281 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xRawRep1 GM78 YY1 PCR1 1 YY1_(SC-281) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-15 2011-11-15 wgEncodeEH001657 1657 GSM803406 Myers HudsonAlpha SL1475 PCR1x 1 exp wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xRawRep1 None RawSignal YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 YY1 281 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Usf1Pcr2xRawRep2 GM78 USF1 PCR2 2 USF-1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001468 1468 GSM803347 Myers HudsonAlpha SL483 PCR2x 2 exp wgEncodeHaibTfbsGm12878Usf1Pcr2xRawRep2 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 USF-1 PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Usf1Pcr2xRawRep1 GM78 USF1 PCR2 1 USF-1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001468 1468 GSM803347 Myers HudsonAlpha SL448 PCR2x 1 exp wgEncodeHaibTfbsGm12878Usf1Pcr2xRawRep1 None RawSignal The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 USF-1 PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf3Pcr1xRawRep2 GM78 TCF3 PCR1 2 TCF3_(SC-349) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002315 2315 GSM1010745 Myers HudsonAlpha SL633 PCR1x 2 exp wgEncodeHaibTfbsGm12878Tcf3Pcr1xRawRep2 None RawSignal Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 TCF3 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf3Pcr1xRawRep1 GM78 TCF3 PCR1 1 TCF3_(SC-349) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002315 2315 GSM1010745 Myers HudsonAlpha SL480 PCR1x 1 exp wgEncodeHaibTfbsGm12878Tcf3Pcr1xRawRep1 None RawSignal Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 TCF3 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf12Pcr1xRawRep2 GM78 TCF12 PCR1 2 TCF12 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001485 1485 GSM803389 Myers HudsonAlpha SL1019 PCR1x 2 exp wgEncodeHaibTfbsGm12878Tcf12Pcr1xRawRep2 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 TCF12 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf12Pcr1xRawRep1 GM78 TCF12 PCR1 1 TCF12 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001485 1485 GSM803389 Myers HudsonAlpha SL673 PCR1x 1 exp wgEncodeHaibTfbsGm12878Tcf12Pcr1xRawRep1 None RawSignal The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 TCF12 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Taf1Pcr1xRawRep2 GM78 TAF1 PCR1 2 TAF1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2009-10-29 2010-07-29 wgEncodeEH001478 1478 GSM803537 Myers HudsonAlpha SL1062 PCR1x 2 exp wgEncodeHaibTfbsGm12878Taf1Pcr1xRawRep2 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 TAF1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Taf1Pcr1xRawRep1 GM78 TAF1 PCR1 1 TAF1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001478 1478 GSM803537 Myers HudsonAlpha SL805 PCR1x 1 exp wgEncodeHaibTfbsGm12878Taf1Pcr1xRawRep1 None RawSignal TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 TAF1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Stat5asc74442V0422111RawRep2 GM78 STAT5A V11 2 STAT5A_(SC-74442) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002321 2321 GSM1010721 Myers HudsonAlpha SL8127 v042211.1 2 exp wgEncodeHaibTfbsGm12878Stat5asc74442V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 STAT5A v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Stat5asc74442V0422111RawRep1 GM78 STAT5A V11 1 STAT5A_(SC-74442) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002321 2321 GSM1010721 Myers HudsonAlpha SL7897 v042211.1 1 exp wgEncodeHaibTfbsGm12878Stat5asc74442V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 STAT5A v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfV0416101RawRep2 GM78 SRF V101 2 SRF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001624 1624 GSM803477 Myers HudsonAlpha SL3827 v041610.1 2 exp wgEncodeHaibTfbsGm12878SrfV0416101RawRep2 None RawSignal Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SRF v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfV0416101RawRep1 GM78 SRF V101 1 SRF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001624 1624 GSM803477 Myers HudsonAlpha SL3578 v041610.1 1 exp wgEncodeHaibTfbsGm12878SrfV0416101RawRep1 None RawSignal Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SRF v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfPcr2xRawRep2 GM78 SRF PCR2 2 SRF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001464 1464 GSM803350 Myers HudsonAlpha SL292 PCR2x 2 exp wgEncodeHaibTfbsGm12878SrfPcr2xRawRep2 None RawSignal Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SRF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfPcr2xRawRep1 GM78 SRF PCR2 1 SRF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001464 1464 GSM803350 Myers HudsonAlpha SL291 PCR2x 1 exp wgEncodeHaibTfbsGm12878SrfPcr2xRawRep1 None RawSignal Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SRF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Sp1Pcr1xRawRep2 GM78 SP1 PCR1 2 SP1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001496 1496 GSM803363 Myers HudsonAlpha SL846 PCR1x 2 exp wgEncodeHaibTfbsGm12878Sp1Pcr1xRawRep2 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SP1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Sp1Pcr1xRawRep1 GM78 SP1 PCR1 1 SP1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001496 1496 GSM803363 Myers HudsonAlpha SL746 PCR1x 1 exp wgEncodeHaibTfbsGm12878Sp1Pcr1xRawRep1 None RawSignal SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SP1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Six5Pcr1xRawRep2 GM78 SIX5 PCR1 2 SIX5 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001542 1542 GSM803338 Myers HudsonAlpha SL1200 PCR1x 2 exp wgEncodeHaibTfbsGm12878Six5Pcr1xRawRep2 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SIX5 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Six5Pcr1xRawRep1 GM78 SIX5 PCR1 1 SIX5 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001542 1542 GSM803338 Myers HudsonAlpha SL1061 PCR1x 1 exp wgEncodeHaibTfbsGm12878Six5Pcr1xRawRep1 None RawSignal The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 SIX5 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxraPcr1xRawRep2 GM78 RXRA PCR1 2 RXRA GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001541 1541 GSM803341 Myers HudsonAlpha SL1265 PCR1x 2 exp wgEncodeHaibTfbsGm12878RxraPcr1xRawRep2 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 RXRA PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxraPcr1xRawRep1 GM78 RXRA PCR1 1 RXRA GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001541 1541 GSM803341 Myers HudsonAlpha SL1063 PCR1x 1 exp wgEncodeHaibTfbsGm12878RxraPcr1xRawRep1 None RawSignal Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 RXRA PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Runx3sc101553V0422111RawRep2 GM78 RUNX3 V11 2 RUNX3_(SC-101553) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002330 2330 GSM1010893 Myers HudsonAlpha SL8128 v042211.1 2 exp wgEncodeHaibTfbsGm12878Runx3sc101553V0422111RawRep2 None RawSignal This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Multiple transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 RUNX3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Runx3sc101553V0422111RawRep1 GM78 RUNX3 V11 1 RUNX3_(SC-101553) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002330 2330 GSM1010893 Myers HudsonAlpha SL7898 v042211.1 1 exp wgEncodeHaibTfbsGm12878Runx3sc101553V0422111RawRep1 None RawSignal This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Multiple transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 RUNX3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Rad21V0416101RawRep2 GM78 RAD21 V101 2 Rad21 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001640 1640 GSM803416 Myers HudsonAlpha SL3934 v041610.1 2 exp wgEncodeHaibTfbsGm12878Rad21V0416101RawRep2 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 RAD21 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Rad21V0416101RawRep1 GM78 RAD21 V101 1 Rad21 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001640 1640 GSM803416 Myers HudsonAlpha SL3933 v041610.1 1 exp wgEncodeHaibTfbsGm12878Rad21V0416101RawRep1 None RawSignal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 RAD21 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pu1Pcr1xRawRep3 GM78 PU.1 PCR1 3 PU.1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH001476 1476 GSM803531 Myers HudsonAlpha SL963 PCR1x 3 exp wgEncodeHaibTfbsGm12878Pu1Pcr1xRawRep3 None RawSignal PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PU.1 PCR1x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pu1Pcr1xRawRep2 GM78 PU.1 PCR1 2 PU.1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001476 1476 GSM803531 Myers HudsonAlpha SL649 PCR1x 2 exp wgEncodeHaibTfbsGm12878Pu1Pcr1xRawRep2 None RawSignal PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PU.1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pu1Pcr1xRawRep1 GM78 PU.1 PCR1 1 PU.1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001476 1476 GSM803531 Myers HudsonAlpha SL612 PCR1x 1 exp wgEncodeHaibTfbsGm12878Pu1Pcr1xRawRep1 None RawSignal PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PU.1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pou2f2Pcr1xRawRep3 GM78 POU2F2 3 POU2F2 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH001475 1475 GSM803534 Myers HudsonAlpha SL851 PCR1x 3 exp wgEncodeHaibTfbsGm12878Pou2f2Pcr1xRawRep3 None RawSignal Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 POU2F2 PCR1x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pou2f2Pcr1xRawRep2 GM78 POU2F2 2 POU2F2 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001475 1475 GSM803534 Myers HudsonAlpha SL648 PCR1x 2 exp wgEncodeHaibTfbsGm12878Pou2f2Pcr1xRawRep2 None RawSignal Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 POU2F2 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pou2f2Pcr1xRawRep1 GM78 POU2F2 1 POU2F2 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001475 1475 GSM803534 Myers HudsonAlpha SL614 PCR1x 1 exp wgEncodeHaibTfbsGm12878Pou2f2Pcr1xRawRep1 None RawSignal Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 POU2F2 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol24h8Pcr1xRawRep2 GM78 Pol2-4H8 PCR1 2 Pol2-4H8 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-21 2011-12-21 wgEncodeEH001517 1517 GSM803485 Myers HudsonAlpha SL847 PCR1x 2 exp wgEncodeHaibTfbsGm12878Pol24h8Pcr1xRawRep2 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Pol2-4H8 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol24h8Pcr1xRawRep1 GM78 Pol2-4H8 PCR1 1 Pol2-4H8 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001517 1517 GSM803485 Myers HudsonAlpha SL748 PCR1x 1 exp wgEncodeHaibTfbsGm12878Pol24h8Pcr1xRawRep1 None RawSignal This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Pol2-4H8 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol2Pcr2xRawRep2 GM78 Pol2 PCR2 2 Pol2 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001463 1463 GSM803355 Myers HudsonAlpha SL209 PCR2x 2 exp wgEncodeHaibTfbsGm12878Pol2Pcr2xRawRep2 None RawSignal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Pol2 PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol2Pcr2xRawRep1 GM78 Pol2 PCR2 1 Pol2 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001463 1463 GSM803355 Myers HudsonAlpha SL207 PCR2x 1 exp wgEncodeHaibTfbsGm12878Pol2Pcr2xRawRep1 None RawSignal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Pol2 PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pmlsc71910V0422111RawRep2 GM78 PML V11 2 PML_(SC-71910) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002308 2308 GSM1010771 Myers HudsonAlpha SL7831 v042211.1 2 exp wgEncodeHaibTfbsGm12878Pmlsc71910V0422111RawRep2 None RawSignal The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PML v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pmlsc71910V0422111RawRep1 GM78 PML V11 1 PML_(SC-71910) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002308 2308 GSM1010771 Myers HudsonAlpha SL7281 v042211.1 1 exp wgEncodeHaibTfbsGm12878Pmlsc71910V0422111RawRep1 None RawSignal The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PML v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pbx3Pcr1xRawRep2 GM78 PBx3 PCR1 2 Pbx3 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001477 1477 GSM803532 Myers HudsonAlpha SL647 PCR1x 2 exp wgEncodeHaibTfbsGm12878Pbx3Pcr1xRawRep2 None RawSignal Pbx 3 (D-17) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PBx3 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pbx3Pcr1xRawRep1 GM78 PBx3 PCR1 1 Pbx3 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001477 1477 GSM803532 Myers HudsonAlpha SL615 PCR1x 1 exp wgEncodeHaibTfbsGm12878Pbx3Pcr1xRawRep1 None RawSignal Pbx 3 (D-17) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PBx3 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5n19Pcr1xRawRep2 GM78 PAX5 PCR1 2 PAX5-N19 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001495 1495 GSM803362 Myers HudsonAlpha SL848 PCR1x 2 exp wgEncodeHaibTfbsGm12878Pax5n19Pcr1xRawRep2 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PAX5-N19 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5n19Pcr1xRawRep1 GM78 PAX5 PCR1 1 PAX5-N19 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001495 1495 GSM803362 Myers HudsonAlpha SL677 PCR1x 1 exp wgEncodeHaibTfbsGm12878Pax5n19Pcr1xRawRep1 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PAX5-N19 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5c20Pcr1xRawRep2 GM78 PAX5 PCR1 2 PAX5-C20 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001489 1489 GSM803391 Myers HudsonAlpha SL735 PCR1x 2 exp wgEncodeHaibTfbsGm12878Pax5c20Pcr1xRawRep2 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PAX5-C20 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5c20Pcr1xRawRep1 GM78 PAX5 PCR1 1 PAX5-C20 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001489 1489 GSM803391 Myers HudsonAlpha SL675 PCR1x 1 exp wgEncodeHaibTfbsGm12878Pax5c20Pcr1xRawRep1 None RawSignal This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 PAX5-C20 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878P300Pcr1xRawRep2 GM78 p300 PCR1 2 p300 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001487 1487 GSM803387 Myers HudsonAlpha SL564 PCR1x 2 exp wgEncodeHaibTfbsGm12878P300Pcr1xRawRep2 None RawSignal EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 p300 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878P300Pcr1xRawRep1 GM78 p300 PCR1 1 p300 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001487 1487 GSM803387 Myers HudsonAlpha SL551 PCR1x 1 exp wgEncodeHaibTfbsGm12878P300Pcr1xRawRep1 None RawSignal EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 p300 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr2xRawRep2 GM78 NRSF PCR2 2 NRSF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001465 1465 GSM803349 Myers HudsonAlpha SL204 PCR2x 2 exp wgEncodeHaibTfbsGm12878NrsfPcr2xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NRSF PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr2xRawRep1 GM78 NRSF PCR2 1 NRSF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001465 1465 GSM803349 Myers HudsonAlpha SL202 PCR2x 1 exp wgEncodeHaibTfbsGm12878NrsfPcr2xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NRSF PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr1xRawRep2 GM78 NRSF PCR1 2 NRSF GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002314 2314 GSM1010744 Myers HudsonAlpha SL7333 PCR1x 2 exp wgEncodeHaibTfbsGm12878NrsfPcr1xRawRep2 None RawSignal Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NRSF PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr1xRawRep1 GM78 NRSF PCR1 1 NRSF GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002314 2314 GSM1010744 Myers HudsonAlpha SL852 PCR1x 1 exp wgEncodeHaibTfbsGm12878NrsfPcr1xRawRep1 None RawSignal Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NRSF PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nficsc81335V0422111RawRep2 GM78 NFIC V11 2 NFIC_(SC-81335) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002343 2343 GSM1010881 Myers HudsonAlpha SL8392 v042211.1 2 exp wgEncodeHaibTfbsGm12878Nficsc81335V0422111RawRep2 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NFIC v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nficsc81335V0422111RawRep1 GM78 NFIC V11 1 NFIC_(SC-81335) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002343 2343 GSM1010881 Myers HudsonAlpha SL8083 v042211.1 1 exp wgEncodeHaibTfbsGm12878Nficsc81335V0422111RawRep1 None RawSignal Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NFIC v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111RawRep2 GM78 NFATC1 V11 2 NFATC1_(SC-17834) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002307 2307 GSM1010779 Myers HudsonAlpha SL7830 v042211.1 2 exp wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111RawRep2 None RawSignal The product of this gene is a component of the nuclear factor of activated T cells DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation, and an inducible nuclear component. Proteins belonging to this family of transcription factors play a central role in inducible gene transcription during immune response. The product of this gene is an inducible nuclear component. It functions as a major molecular target for the immunosuppressive drugs such as cyclosporin A. Five transcript variants encoding distinct isoforms have been identified for this gene. Different isoforms of this protein may regulate inducible expression of different cytokine genes. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NFATC1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111RawRep1 GM78 NFATC1 V11 1 NFATC1_(SC-17834) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002307 2307 GSM1010779 Myers HudsonAlpha SL7280 v042211.1 1 exp wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111RawRep1 None RawSignal The product of this gene is a component of the nuclear factor of activated T cells DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation, and an inducible nuclear component. Proteins belonging to this family of transcription factors play a central role in inducible gene transcription during immune response. The product of this gene is an inducible nuclear component. It functions as a major molecular target for the immunosuppressive drugs such as cyclosporin A. Five transcript variants encoding distinct isoforms have been identified for this gene. Different isoforms of this protein may regulate inducible expression of different cytokine genes. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 NFATC1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mta3sc81325V0422111RawRep2 GM78 MTA3 V11 2 MTA3_(SC-81325) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002329 2329 GSM1010729 Myers HudsonAlpha SL8129 v042211.1 2 exp wgEncodeHaibTfbsGm12878Mta3sc81325V0422111RawRep2 None RawSignal Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 MTA3 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mta3sc81325V0422111RawRep1 GM78 MTA3 V11 1 MTA3_(SC-81325) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002329 2329 GSM1010729 Myers HudsonAlpha SL7899 v042211.1 1 exp wgEncodeHaibTfbsGm12878Mta3sc81325V0422111RawRep1 None RawSignal Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 MTA3 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2csc13268V0416101RawRep2 GM78 MEFC V101 2 MEF2C_(SC-13268) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001648 1648 GSM803420 Myers HudsonAlpha SL2127 v041610.1 2 exp wgEncodeHaibTfbsGm12878Mef2csc13268V0416101RawRep2 None RawSignal This locus encodes a member of the MADS box transcription enhancer factor 2 (MEF2) family of proteins, which play a role in myogenesis. The encoded protein, MEF2 polypeptide C, has both trans-activating and DNA binding activities. This protein may play a role in maintaining the differentiated state of muscle cells. Mutations and deletions at this locus have been associated with severe mental retardation, stereotypic movements, epilepsy, and cerebral malformation. Alternatively spliced transcript variants have been described. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 MEF2C v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2csc13268V0416101RawRep1 GM78 MEFC V101 1 MEF2C_(SC-13268) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001648 1648 GSM803420 Myers HudsonAlpha SL1654 v041610.1 1 exp wgEncodeHaibTfbsGm12878Mef2csc13268V0416101RawRep1 None RawSignal This locus encodes a member of the MADS box transcription enhancer factor 2 (MEF2) family of proteins, which play a role in myogenesis. The encoded protein, MEF2 polypeptide C, has both trans-activating and DNA binding activities. This protein may play a role in maintaining the differentiated state of muscle cells. Mutations and deletions at this locus have been associated with severe mental retardation, stereotypic movements, epilepsy, and cerebral malformation. Alternatively spliced transcript variants have been described. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 MEF2C v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2aPcr1xRawRep2 GM78 MEF2A PCR1 2 MEF2A GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001565 1565 GSM803511 Myers HudsonAlpha SL1792 PCR1x 2 exp wgEncodeHaibTfbsGm12878Mef2aPcr1xRawRep2 None RawSignal The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 MEF2A PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2aPcr1xRawRep1 GM78 MEF2A PCR1 1 MEF2A GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001565 1565 GSM803511 Myers HudsonAlpha SL1425 PCR1x 1 exp wgEncodeHaibTfbsGm12878Mef2aPcr1xRawRep1 None RawSignal The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 MEF2A PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xRawRep2 GM78 IRF4 PCR1 2 IRF4_(SC-6059) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001484 1484 GSM803390 Myers HudsonAlpha SL951 PCR1x 2 exp wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xRawRep2 None RawSignal The protein encoded by this gene belongs to the IRF (interferon regulatory factor) family. It functions as a lymphocyte specific transcription factor and negatively regulates TLR signaling by selectively competing with IRF5. A chromosomal translocation involving this gene and the IgH locus, t(6;14)(p25;q32), may be a cause of multiple myeloma (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 IRF4 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xRawRep1 GM78 IRF4 PCR1 1 IRF4_(SC-6059) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001484 1484 GSM803390 Myers HudsonAlpha SL838 PCR1x 1 exp wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xRawRep1 None RawSignal The protein encoded by this gene belongs to the IRF (interferon regulatory factor) family. It functions as a lymphocyte specific transcription factor and negatively regulates TLR signaling by selectively competing with IRF5. A chromosomal translocation involving this gene and the IgH locus, t(6;14)(p25;q32), may be a cause of multiple myeloma (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 IRF4 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878GabpPcr2xRawRep2 GM78 GABP PCR2 2 GABP GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001462 1462 GSM803356 Myers HudsonAlpha SL205 PCR2x 2 exp wgEncodeHaibTfbsGm12878GabpPcr2xRawRep2 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 GABP PCR2x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878GabpPcr2xRawRep1 GM78 GABP PCR2 1 GABP GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001462 1462 GSM803356 Myers HudsonAlpha SL203 PCR2x 1 exp wgEncodeHaibTfbsGm12878GabpPcr2xRawRep1 None RawSignal The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 GABP PCR2x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Foxm1sc502V0422111RawRep2 GM78 FOXM1 V11 2 FOXM1_(SC-502) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002529 2529 GSM1010731 Myers HudsonAlpha SL7834 v042211.1 2 exp wgEncodeHaibTfbsGm12878Foxm1sc502V0422111RawRep2 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 FOXM1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Foxm1sc502V0422111RawRep1 GM78 FOXM1 V11 1 FOXM1_(SC-502) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002529 2529 GSM1010731 Myers HudsonAlpha SL7551 v042211.1 1 exp wgEncodeHaibTfbsGm12878Foxm1sc502V0422111RawRep1 None RawSignal The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 FOXM1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ets1Pcr1xRawRep2 GM78 ETS1 PCR1 2 ETS1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-08 wgEncodeEH001564 1564 GSM803510 Myers HudsonAlpha SL1655 PCR1x 2 exp wgEncodeHaibTfbsGm12878Ets1Pcr1xRawRep2 None RawSignal ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ETS1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ets1Pcr1xRawRep1 GM78 ETS1 PCR1 1 ETS1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001564 1564 GSM803510 Myers HudsonAlpha SL1507 PCR1x 1 exp wgEncodeHaibTfbsGm12878Ets1Pcr1xRawRep1 None RawSignal ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ETS1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Elf1sc631V0416101RawRep2 GM78 ELF1 V101 2 ELF1_(SC-631) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001617 1617 GSM803496 Myers HudsonAlpha SL3352 v041610.1 2 exp wgEncodeHaibTfbsGm12878Elf1sc631V0416101RawRep2 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ELF1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Elf1sc631V0416101RawRep1 GM78 ELF1 V101 1 ELF1_(SC-631) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001617 1617 GSM803496 Myers HudsonAlpha SL2253 v041610.1 1 exp wgEncodeHaibTfbsGm12878Elf1sc631V0416101RawRep1 None RawSignal This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ELF1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Egr1V0416101RawRep2 GM78 Egr-1 V101 2 Egr-1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001632 1632 GSM803434 Myers HudsonAlpha SL3828 v041610.1 2 exp wgEncodeHaibTfbsGm12878Egr1V0416101RawRep2 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Egr-1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Egr1V0416101RawRep1 GM78 Egr-1 V101 1 Egr-1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001632 1632 GSM803434 Myers HudsonAlpha SL3579 v041610.1 1 exp wgEncodeHaibTfbsGm12878Egr1V0416101RawRep1 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Egr-1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Egr1Pcr2xRawRep3 GM78 Egr-1 PCR2 3 Egr-1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002328 2328 GSM1010730 Myers HudsonAlpha SL482 PCR2x 3 exp wgEncodeHaibTfbsGm12878Egr1Pcr2xRawRep3 None RawSignal Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Egr-1 PCR2x ChIP-seq Raw Signal Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ebf1sc137065Pcr1xRawRep2 GM78 EBF1 PCR1 2 EBF1_(SC-137065) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001480 1480 GSM803386 Myers HudsonAlpha SL988 PCR1x 2 exp wgEncodeHaibTfbsGm12878Ebf1sc137065Pcr1xRawRep2 None RawSignal Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 EBF1 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ebf1sc137065Pcr1xRawRep1 GM78 EBF1 PCR1 1 EBF1_(SC-137065) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001480 1480 GSM803386 Myers HudsonAlpha SL745 PCR1x 1 exp wgEncodeHaibTfbsGm12878Ebf1sc137065Pcr1xRawRep1 None RawSignal Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 EBF1 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Creb1sc240V0422111RawRep2 GM78 CREB1 V11 2 CREB1_(SC-240) GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003275 3275 GSM1010760 Myers HudsonAlpha SL16741 v042211.1 2 exp wgEncodeHaibTfbsGm12878Creb1sc240V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 CREB1 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Creb1sc240V0422111RawRep1 GM78 CREB1 V11 1 CREB1_(SC-240) GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003275 3275 GSM1010760 Myers HudsonAlpha SL12408 v042211.1 1 exp wgEncodeHaibTfbsGm12878Creb1sc240V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 CREB1 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Cebpbsc150V0422111RawRep2 GM78 CEBPB V11 2 CEBPB_(SC-150) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003212 3212 GSM1010850 Myers HudsonAlpha SL9542 v042211.1 2 exp wgEncodeHaibTfbsGm12878Cebpbsc150V0422111RawRep2 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 CEBPB v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Cebpbsc150V0422111RawRep1 GM78 CEBPB V11 1 CEBPB_(SC-150) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003212 3212 GSM1010850 Myers HudsonAlpha SL8084 v042211.1 1 exp wgEncodeHaibTfbsGm12878Cebpbsc150V0422111RawRep1 None RawSignal Epitope mapping at the C-terminus of C/EBP-beta of rat origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 CEBPB v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bclaf101388V0416101RawRep2 GM78 BCLAF1 2 BCLAF1_(SC-101388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001563 1563 GSM803509 Myers HudsonAlpha SL2128 v041610.1 2 exp wgEncodeHaibTfbsGm12878Bclaf101388V0416101RawRep2 None RawSignal This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BCLAF1 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bclaf101388V0416101RawRep1 GM78 BCLAF1 1 BCLAF1_(SC-101388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-29 2011-08-28 wgEncodeEH001563 1563 GSM803509 Myers HudsonAlpha SL1509 v041610.1 1 exp wgEncodeHaibTfbsGm12878Bclaf101388V0416101RawRep1 None RawSignal This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BCLAF1 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl3V0416101RawRep2 GM78 BCL3 V101 2 BCL3 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH001658 1658 GSM803342 Myers HudsonAlpha SL3931 v041610.1 2 exp wgEncodeHaibTfbsGm12878Bcl3V0416101RawRep2 None RawSignal This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BCL3 v041610.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl3V0416101RawRep1 GM78 BCL3 V101 1 BCL3 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH001658 1658 GSM803342 Myers HudsonAlpha SL3728 v041610.1 1 exp wgEncodeHaibTfbsGm12878Bcl3V0416101RawRep1 None RawSignal This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BCL3 v041610.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl11aPcr1xRawRep2 GM78 BCL11A 2 BCL11A GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001486 1486 GSM803388 Myers HudsonAlpha SL976 PCR1x 2 exp wgEncodeHaibTfbsGm12878Bcl11aPcr1xRawRep2 None RawSignal This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BCL11A PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl11aPcr1xRawRep1 GM78 BCL11A 1 BCL11A GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001486 1486 GSM803388 Myers HudsonAlpha SL650 PCR1x 1 exp wgEncodeHaibTfbsGm12878Bcl11aPcr1xRawRep1 None RawSignal This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BCL11A PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878BatfPcr1xRawRep2 GM78 BATF PCR1 2 BATF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-11-30 2011-08-30 wgEncodeEH001479 1479 GSM803538 Myers HudsonAlpha SL985 PCR1x 2 exp wgEncodeHaibTfbsGm12878BatfPcr1xRawRep2 None RawSignal The protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BATF PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878BatfPcr1xRawRep1 GM78 BATF PCR1 1 BATF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-01 2011-09-01 wgEncodeEH001479 1479 GSM803538 Myers HudsonAlpha SL839 PCR1x 1 exp wgEncodeHaibTfbsGm12878BatfPcr1xRawRep1 None RawSignal The protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 BATF PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf3Pcr1xRawRep2 GM78 ATF3 PCR1 2 ATF3 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001562 1562 GSM803508 Myers HudsonAlpha SL1508 PCR1x 2 exp wgEncodeHaibTfbsGm12878Atf3Pcr1xRawRep2 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ATF3 PCR1x ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf3Pcr1xRawRep1 GM78 ATF3 PCR1 1 ATF3 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001562 1562 GSM803508 Myers HudsonAlpha SL1269 PCR1x 1 exp wgEncodeHaibTfbsGm12878Atf3Pcr1xRawRep1 None RawSignal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ATF3 PCR1x ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf2sc81188V0422111RawRep2 GM78 ATF2 V11 2 ATF2_(SC-81188) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002306 2306 GSM1010780 Myers HudsonAlpha SL7561 v042211.1 2 exp wgEncodeHaibTfbsGm12878Atf2sc81188V0422111RawRep2 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ATF2 v042211.1 ChIP-seq Raw Signal Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf2sc81188V0422111RawRep1 GM78 ATF2 V11 1 ATF2_(SC-81188) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002306 2306 GSM1010780 Myers HudsonAlpha SL7282 v042211.1 1 exp wgEncodeHaibTfbsGm12878Atf2sc81188V0422111RawRep1 None RawSignal This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 ATF2 v042211.1 ChIP-seq Raw Signal Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsViewPeaks Peaks Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87Pol24h8V0416101PkRep2V2 U87 Pol2-4H8 V101 2 Pol2-4H8 U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-23 2011-05-20 2012-02-20 wgEncodeEH001674 1674 GSM803459 Myers HudsonAlpha SL3773 v041610.1 2 exp MACS wgEncodeHaibTfbsU87Pol24h8V0416101PkRep2V2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment U87 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87Pol24h8V0416101PkRep1V2 U87 Pol2-4H8 V101 1 Pol2-4H8 U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-23 2011-05-20 2012-02-23 wgEncodeEH001674 1674 GSM803459 Myers HudsonAlpha SL1962 v041610.1 1 exp MACS wgEncodeHaibTfbsU87Pol24h8V0416101PkRep1V2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment U87 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87NrsfPcr2xPkRep2V2 U87 NRSF PCR2 2 NRSF U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-24 2011-01-21 2011-10-20 wgEncodeEH001554 1554 GSM803372 Myers HudsonAlpha SL413 PCR2x 2 exp MACS wgEncodeHaibTfbsU87NrsfPcr2xPkRep2V2 None Peaks Neuron-restrictive silencer transcription factor glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment U87 NRSF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsU87NrsfPcr2xPkRep1V2 U87 NRSF PCR2 1 NRSF U87 ChipSeq ENCODE Mar 2012 Freeze 2012-01-24 2011-03-08 2011-12-08 wgEncodeEH001554 1554 GSM803372 Myers HudsonAlpha SL88 PCR2x 1 exp MACS wgEncodeHaibTfbsU87NrsfPcr2xPkRep1V2 None Peaks Neuron-restrictive silencer transcription factor glioblastoma, astrocytoma, (PMID: 4332744) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment U87 NRSF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dP300V0416102Dm002p1hPkRep2 T47D p300 DMSO 2 p300 T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-12-11 2011-09-11 wgEncodeEH001602 1602 GSM803522 Myers HudsonAlpha SL3015 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dP300V0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks EP300(c-20) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D p300 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dP300V0416102Dm002p1hPkRep1 T47D p300 DMSO 1 p300 T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-12-11 2011-09-11 wgEncodeEH001602 1602 GSM803522 Myers HudsonAlpha SL2633 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dP300V0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks EP300(c-20) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D p300 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dJundV0422111PkRep2 T47D JunD V11 2 JunD T-47D ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003321 3321 GSM1010718 Myers HudsonAlpha SL11657 v042211.1 2 exp MACS wgEncodeHaibTfbsT47dJundV0422111PkRep2 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment T-47D JunD v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dJundV0422111PkRep1 T47D JunD V11 1 JunD T-47D ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003321 3321 GSM1010718 Myers HudsonAlpha SL11656 v042211.1 1 exp MACS wgEncodeHaibTfbsT47dJundV0422111PkRep1 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment T-47D JunD v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hPkRep2 T47D GATA3 DMSO 2 GATA3_(SC-268) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001639 1639 GSM803514 Myers HudsonAlpha SL3013 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D GATA3 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hPkRep1 T47D GATA3 DMSO 1 GATA3_(SC-268) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001639 1639 GSM803514 Myers HudsonAlpha SL2636 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dGata3sc268V0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D GATA3 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hPkRep2 T47D FOXA1 DMSO 2 FOXA1_(SC-6553) T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001588 1588 GSM803409 Myers HudsonAlpha SL2081 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D FOXA1 6553 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hPkRep1 T47D FOXA1 DMSO 1 FOXA1_(SC-6553) T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001588 1588 GSM803409 Myers HudsonAlpha SL1878 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dFoxa1sc6553V0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D FOXA1 6553 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hPkRep2 T47 ERa Gen PC2 2 ERalpha_a T-47D ChipSeq ENCODE June 2010 Freeze 2010-06-22 2011-03-22 wgEncodeEH001556 1556 GSM803374 Myers HudsonAlpha SL1492 Genestein 100nM treatment hg19 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hPkRep2 Genistein_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Regions of enriched signal in experiment T-47D ERa a Genistein PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hPkRep1 T47 ERa Gen PC2 1 ERalpha_a T-47D ChipSeq ENCODE June 2010 Freeze 2010-06-22 2011-03-22 wgEncodeEH001556 1556 GSM803374 Myers HudsonAlpha SL1218 Genestein 100nM treatment hg19 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hPkRep1 Genistein_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Regions of enriched signal in experiment T-47D ERa a Genistein PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hPkRep2 T47D ERa Estra 2 ERalpha_a T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-09-28 2011-06-28 wgEncodeEH001577 1577 GSM803539 Myers HudsonAlpha SL1491 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hPkRep2 Estradiol_10nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Regions of enriched signal in experiment T-47D ERa a Estradiol v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hPkRep1 T47D ERa Estra 1 ERalpha_a T-47D ChipSeq ENCODE Jan 2011 Freeze 2010-09-28 2011-06-28 wgEncodeEH001577 1577 GSM803539 Myers HudsonAlpha SL1217 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dEralphaaV0416102Est10nm1hPkRep1 Estradiol_10nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Regions of enriched signal in experiment T-47D ERa a Estradiol v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEraaV0416102Bpa1hPkRep2 T47D ERa BPA 2 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002299 2299 GSM1010823 Myers HudsonAlpha SL1877 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dEraaV0416102Bpa1hPkRep2 BPA_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Regions of enriched signal in experiment T-47D ERa a BPA v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dEraaV0416102Bpa1hPkRep1 T47D ERa BPA 1 ERalpha_a T-47D ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002299 2299 GSM1010823 Myers HudsonAlpha SL1493 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dEraaV0416102Bpa1hPkRep1 BPA_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Regions of enriched signal in experiment T-47D ERa a BPA v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hPkRep2 T47D CTCF DMSO 2 CTCF_(SC-5916) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001656 1656 GSM803348 Myers HudsonAlpha SL3014 v041610.2 2 exp MACS wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D CTCF 5916 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hPkRep1 T47D CTCF DMSO 1 CTCF_(SC-5916) T-47D ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001656 1656 GSM803348 Myers HudsonAlpha SL2634 v041610.2 1 exp MACS wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a mammary ductal carcinoma. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment T-47D CTCF 5916 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraYy1sc281V0416102PkRep2 SKRA YY1 V102 2 YY1_(SC-281) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001615 1615 GSM803498 Myers HudsonAlpha SL3640 v041610.2 2 exp MACS wgEncodeHaibTfbsSknshraYy1sc281V0416102PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA YY1 281 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraYy1sc281V0416102PkRep1 SKRA YY1 V102 1 YY1_(SC-281) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001615 1615 GSM803498 Myers HudsonAlpha SL3639 v041610.2 1 exp MACS wgEncodeHaibTfbsSknshraYy1sc281V0416102PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA YY1 281 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraUsf1sc8983V0416102PkRep2 SKRA USF1 V102 2 USF1_(SC-8983) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001621 1621 GSM803472 Myers HudsonAlpha SL2919 v041610.2 2 exp MACS wgEncodeHaibTfbsSknshraUsf1sc8983V0416102PkRep2 None Peaks This gene encodes a member of the basic helix-loop-helix leucine zipper family, and can function as a cellular transcription factor. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs. This gene has been linked to familial combined hyperlipidemia (FCHL). Two transcript variants encoding distinct isoforms have been identified for this gene. (provided by RefSeq). neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA USF-1 8983 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraUsf1sc8983V0416102PkRep1 SKRA USF1 V102 1 USF1_(SC-8983) SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001621 1621 GSM803472 Myers HudsonAlpha SL2911 v041610.2 1 exp MACS wgEncodeHaibTfbsSknshraUsf1sc8983V0416102PkRep1 None Peaks This gene encodes a member of the basic helix-loop-helix leucine zipper family, and can function as a cellular transcription factor. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs. This gene has been linked to familial combined hyperlipidemia (FCHL). Two transcript variants encoding distinct isoforms have been identified for this gene. (provided by RefSeq). neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA USF-1 8983 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraRad21V0416102PkRep2 SKRA RAD21 V102 2 Rad21 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001614 1614 GSM803497 Myers HudsonAlpha SL2915 v041610.2 2 exp MACS wgEncodeHaibTfbsSknshraRad21V0416102PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA RAD21 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraRad21V0416102PkRep1 SKRA RAD21 V102 1 Rad21 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001614 1614 GSM803497 Myers HudsonAlpha SL2907 v041610.2 1 exp MACS wgEncodeHaibTfbsSknshraRad21V0416102PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA RAD21 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraP300V0416102PkRep2 SKRA p300 V102 2 p300 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001616 1616 GSM803495 Myers HudsonAlpha SL2918 v041610.2 2 exp MACS wgEncodeHaibTfbsSknshraP300V0416102PkRep2 None Peaks EP300(c-20) neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA p300 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraP300V0416102PkRep1 SKRA p300 V102 1 p300 SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001616 1616 GSM803495 Myers HudsonAlpha SL2910 v041610.2 1 exp MACS wgEncodeHaibTfbsSknshraP300V0416102PkRep1 None Peaks EP300(c-20) neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA p300 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraCtcfV0416102PkRep2 SKRA CTCF V102 2 CTCF SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001613 1613 GSM803333 Myers HudsonAlpha SL2914 v041610.2 2 exp MACS wgEncodeHaibTfbsSknshraCtcfV0416102PkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA CTCF v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshraCtcfV0416102PkRep1 SKRA CTCF V102 1 CTCF SK-N-SH_RA ChipSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH001613 1613 GSM803333 Myers HudsonAlpha SL2906 v041610.2 1 exp MACS wgEncodeHaibTfbsSknshraCtcfV0416102PkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH RA CTCF v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcPol24h8V0416101PkRep2 SKMC Pol2-4H8 V101 2 Pol2-4H8 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002281 2281 GSM1010793 Myers HudsonAlpha SL5611 v041610.1 2 exp MACS wgEncodeHaibTfbsSknmcPol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-MC Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcPol24h8V0416101PkRep1 SKMC Pol2-4H8 V101 1 Pol2-4H8 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002281 2281 GSM1010793 Myers HudsonAlpha SL1963 v041610.1 1 exp MACS wgEncodeHaibTfbsSknmcPol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-MC Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcFoxp2Pcr2xPkRep2 SKMC FOXP2 PCR2 2 FOXP2 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2008-10-31 2009-07-31 wgEncodeEH001461 1461 GSM803353 Myers HudsonAlpha SL167 PCR2x 2 exp wgEncodeHaibTfbsSknmcFoxp2Pcr2xPkRep2 None Peaks This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment SK-N-MC FOXP2 PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknmcFoxp2Pcr2xPkRep1 SKMC FOXP2 PCR2 1 FOXP2 SK-N-MC ChipSeq ENCODE Mar 2012 Freeze 2011-06-02 2012-03-02 wgEncodeEH001461 1461 GSM803353 Myers HudsonAlpha SL144 PCR2x 1 exp wgEncodeHaibTfbsSknmcFoxp2Pcr2xPkRep1 None Peaks This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment SK-N-MC FOXP2 PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Taf1V0416101PkRep2 PFSK TAF1 V101 2 TAF1 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002309 2309 GSM1010770 Myers HudsonAlpha SL6969 v041610.1 2 exp MACS wgEncodeHaibTfbsPfsk1Taf1V0416101PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 TAF1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Taf1V0416101PkRep1 PFSK TAF1 V101 1 TAF1 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002309 2309 GSM1010770 Myers HudsonAlpha SL3772 v041610.1 1 exp MACS wgEncodeHaibTfbsPfsk1Taf1V0416101PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 TAF1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Sin3ak20V0416101PkRep2 PFSK Sin3A V101 2 Sin3Ak-20 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002268 2268 GSM1010781 Myers HudsonAlpha SL5041 v041610.1 2 exp MACS wgEncodeHaibTfbsPfsk1Sin3ak20V0416101PkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Sin3ak20V0416101PkRep1 PFSK Sin3A V101 1 Sin3Ak-20 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002268 2268 GSM1010781 Myers HudsonAlpha SL2354 v041610.1 1 exp MACS wgEncodeHaibTfbsPfsk1Sin3ak20V0416101PkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Pol24h8V0416101PkRep2 PFSK Pol2-4H8 V101 2 Pol2-4H8 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH002272 2272 GSM1010819 Myers HudsonAlpha SL5610 v041610.1 2 exp MACS wgEncodeHaibTfbsPfsk1Pol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Pol24h8V0416101PkRep1 PFSK Pol2-4H8 V101 1 Pol2-4H8 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH002272 2272 GSM1010819 Myers HudsonAlpha SL2353 v041610.1 1 exp MACS wgEncodeHaibTfbsPfsk1Pol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfV0416101PkRep2 PFSK NRSF V101 2 NRSF PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002267 2267 GSM1010786 Myers HudsonAlpha SL5497 v041610.1 2 exp MACS wgEncodeHaibTfbsPfsk1NrsfV0416101PkRep2 None Peaks Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 NRSF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfV0416101PkRep1 PFSK NRSF V101 1 NRSF PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002267 2267 GSM1010786 Myers HudsonAlpha SL5496 v041610.1 1 exp MACS wgEncodeHaibTfbsPfsk1NrsfV0416101PkRep1 None Peaks Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PFSK-1 NRSF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfPcr2xPkRep2 PFSK NRSF PCR2 2 NRSF PFSK-1 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001553 1553 GSM803369 Myers HudsonAlpha SL411 PCR2x 2 exp MACS wgEncodeHaibTfbsPfsk1NrsfPcr2xPkRep2 None Peaks Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment PFSK-1 NRSF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1NrsfPcr2xPkRep1 PFSK NRSF PCR2 1 NRSF PFSK-1 ChipSeq ENCODE Jan 2011 Freeze 2010-08-06 2011-05-06 wgEncodeEH001553 1553 GSM803369 Myers HudsonAlpha SL149 PCR2x 1 exp MACS wgEncodeHaibTfbsPfsk1NrsfPcr2xPkRep1 None Peaks Neuron-restrictive silencer transcription factor neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment PFSK-1 NRSF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Foxp2Pcr2xPkRep2 PFSK FOXP2 PCR2 2 FOXP2 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2008-10-31 2009-07-31 wgEncodeEH001460 1460 GSM803480 Myers HudsonAlpha SL14 PCR2x 2 exp wgEncodeHaibTfbsPfsk1Foxp2Pcr2xPkRep2 None Peaks This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment PFSK-1 FOXP2 PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPfsk1Foxp2Pcr2xPkRep1 PFSK FOXP2 PCR2 1 FOXP2 PFSK-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-02 2012-03-02 wgEncodeEH001460 1460 GSM803480 Myers HudsonAlpha SL13 PCR2x 1 exp wgEncodeHaibTfbsPfsk1Foxp2Pcr2xPkRep1 None Peaks This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. Transcriptional repressor, involved in the development of speech neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment PFSK-1 FOXP2 PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Sin3ak20V0416101PkRep2 PANC Sin3A V101 2 Sin3Ak-20 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002266 2266 GSM1010785 Myers HudsonAlpha SL5042 v041610.1 2 exp MACS wgEncodeHaibTfbsPanc1Sin3ak20V0416101PkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PANC-1 Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Sin3ak20V0416101PkRep1 PANC Sin3A V101 1 Sin3Ak-20 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002266 2266 GSM1010785 Myers HudsonAlpha SL2344 v041610.1 1 exp MACS wgEncodeHaibTfbsPanc1Sin3ak20V0416101PkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PANC-1 Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Pol24h8V0416101PkRep2 PANC Pol2-4H8 V101 2 Pol2-4H8 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002265 2265 GSM1010788 Myers HudsonAlpha SL5609 v041610.1 2 exp MACS wgEncodeHaibTfbsPanc1Pol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PANC-1 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1Pol24h8V0416101PkRep1 PANC Pol2-4H8 V101 1 Pol2-4H8 PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002265 2265 GSM1010788 Myers HudsonAlpha SL2343 v041610.1 1 exp MACS wgEncodeHaibTfbsPanc1Pol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PANC-1 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0422111PkRep2 PANC NRSF V11 2 NRSF PANC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003285 3285 GSM1010859 Myers HudsonAlpha SL16342 v042211.1 2 exp MACS wgEncodeHaibTfbsPanc1NrsfV0422111PkRep2 None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment PANC-1 NRSF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0422111PkRep1 PANC NRSF V11 1 NRSF PANC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003285 3285 GSM1010859 Myers HudsonAlpha SL14681 v042211.1 1 exp MACS wgEncodeHaibTfbsPanc1NrsfV0422111PkRep1 None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment PANC-1 NRSF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0416101PkRep2 PANC NRSF V101 2 NRSF PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002280 2280 GSM1010792 Myers HudsonAlpha SL5495 v041610.1 2 exp MACS wgEncodeHaibTfbsPanc1NrsfV0416101PkRep2 None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PANC-1 NRSF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfV0416101PkRep1 PANC NRSF V101 1 NRSF PANC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002280 2280 GSM1010792 Myers HudsonAlpha SL4437 v041610.1 1 exp MACS wgEncodeHaibTfbsPanc1NrsfV0416101PkRep1 None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment PANC-1 NRSF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep2 PANC NRSF PCR2 2 NRSF PANC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-08-06 2011-05-06 wgEncodeEH001552 1552 GSM803370 Myers HudsonAlpha SL522 PCR2x 2 exp MACS wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep2 None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment PANC-1 NRSF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep1 PANC NRSF PCR2 1 NRSF PANC-1 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001552 1552 GSM803370 Myers HudsonAlpha SL116 PCR2x 1 exp MACS wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep1 None Peaks Neuron-restrictive silencer transcription factor pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment PANC-1 NRSF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pu1V0422111PkRep2 HL-60 PU.1 V11 2 PU.1 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003292 3292 GSM1010843 Myers HudsonAlpha SL14712 v042211.1 2 exp MACS wgEncodeHaibTfbsHl60Pu1V0422111PkRep2 None Peaks PU.1 (H-135) promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 PU.1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pu1V0422111PkRep1 HL-60 PU.1 V11 1 PU.1 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003292 3292 GSM1010843 Myers HudsonAlpha SL12629 v042211.1 1 exp MACS wgEncodeHaibTfbsHl60Pu1V0422111PkRep1 None Peaks PU.1 (H-135) promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 PU.1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pol24h8V0422111PkRep2 HL-60 Pol2-4H8 V11 2 Pol2-4H8 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003253 3253 GSM1010737 Myers HudsonAlpha SL16322 v042211.1 2 exp MACS wgEncodeHaibTfbsHl60Pol24h8V0422111PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 Pol2-4H8 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60Pol24h8V0422111PkRep1 HL-60 Pol2-4H8 V11 1 Pol2-4H8 HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003253 3253 GSM1010737 Myers HudsonAlpha SL12628 v042211.1 1 exp MACS wgEncodeHaibTfbsHl60Pol24h8V0422111PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 Pol2-4H8 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60NrsfV0422111PkRep2 HL-60 NRSF V11 2 NRSF HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003247 3247 GSM1010754 Myers HudsonAlpha SL13747 v042211.1 2 exp MACS wgEncodeHaibTfbsHl60NrsfV0422111PkRep2 None Peaks Neuron-restrictive silencer transcription factor promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 NRSF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60NrsfV0422111PkRep1 HL-60 NRSF V11 1 NRSF HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003247 3247 GSM1010754 Myers HudsonAlpha SL12632 v042211.1 1 exp MACS wgEncodeHaibTfbsHl60NrsfV0422111PkRep1 None Peaks Neuron-restrictive silencer transcription factor promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 NRSF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60GabpV0422111PkRep2 HL-60 GABP V11 2 GABP HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003252 3252 GSM1010822 Myers HudsonAlpha SL16321 v042211.1 2 exp MACS wgEncodeHaibTfbsHl60GabpV0422111PkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 GABP v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHl60GabpV0422111PkRep1 HL-60 GABP V11 1 GABP HL-60 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003252 3252 GSM1010822 Myers HudsonAlpha SL12633 v042211.1 1 exp MACS wgEncodeHaibTfbsHl60GabpV0422111PkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. promyelocytic leukemia cells, (PMID: 276884) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HL-60 GABP v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Zbtb33V0416101PkRep2 HCT ZBTB33 2 ZBTB33 HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001672 1672 GSM803458 Myers HudsonAlpha SL3970 v041610.1 2 exp MACS wgEncodeHaibTfbsHct116Zbtb33V0416101PkRep2 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HCT-116 ZBTB33 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Zbtb33V0416101PkRep1 HCT ZBTB33 1 ZBTB33 HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001672 1672 GSM803458 Myers HudsonAlpha SL3646 v041610.1 1 exp MACS wgEncodeHaibTfbsHct116Zbtb33V0416101PkRep1 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HCT-116 ZBTB33 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Yy1sc281V0416101PkRep2 HCT YY1 V101 2 YY1_(SC-281) HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001671 1671 GSM803354 Myers HudsonAlpha SL4500 v041610.1 2 exp MACS wgEncodeHaibTfbsHct116Yy1sc281V0416101PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HCT-116 YY1 281 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Yy1sc281V0416101PkRep1 HCT YY1 V101 1 YY1_(SC-281) HCT-116 ChipSeq ENCODE Mar 2012 Freeze 2011-05-20 2012-02-20 wgEncodeEH001671 1671 GSM803354 Myers HudsonAlpha SL3971 v041610.1 1 exp MACS wgEncodeHaibTfbsHct116Yy1sc281V0416101PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HCT-116 YY1 281 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Usf1V0422111PkRep2 HCT USF1 V11 2 USF-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003310 3310 GSM1010836 Myers HudsonAlpha SL16733 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Usf1V0422111PkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 USF-1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Usf1V0422111PkRep1 HCT USF1 V11 1 USF-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003310 3310 GSM1010836 Myers HudsonAlpha SL12238 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Usf1V0422111PkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 USF-1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Tead4sc101184V0422111PkRep2 HCT TEAD4 V11 2 TEAD4_(SC-101184) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003309 3309 GSM1010772 Myers HudsonAlpha SL14570 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Tead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Tead4sc101184V0422111PkRep1 HCT TEAD4 V11 1 TEAD4_(SC-101184) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003309 3309 GSM1010772 Myers HudsonAlpha SL16313 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Tead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116SrfV0422111PkRep2 HCT SRF V11 2 SRF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003218 3218 GSM1010851 Myers HudsonAlpha SL13070 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116SrfV0422111PkRep2 None Peaks Serum response transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 SRF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116SrfV0422111PkRep1 HCT SRF V11 1 SRF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003218 3218 GSM1010851 Myers HudsonAlpha SL12237 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116SrfV0422111PkRep1 None Peaks Serum response transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 SRF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sp1V0422111PkRep2 HCT SP1 V11 2 SP1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003221 3221 GSM1010902 Myers HudsonAlpha SL13072 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Sp1V0422111PkRep2 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 SP1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sp1V0422111PkRep1 HCT SP1 V11 1 SP1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003221 3221 GSM1010902 Myers HudsonAlpha SL12239 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Sp1V0422111PkRep1 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 SP1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sin3ak20V0422111PkRep2 HCT Sin3A V11 2 Sin3Ak-20 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003222 3222 GSM1010905 Myers HudsonAlpha SL13076 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Sin3ak20V0422111PkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 Sin3Ak-20 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Sin3ak20V0422111PkRep1 HCT Sin3A V11 1 Sin3Ak-20 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003222 3222 GSM1010905 Myers HudsonAlpha SL12244 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Sin3ak20V0422111PkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 Sin3Ak-20 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Rad21V0422111PkRep2 HCT RAD21 V11 2 Rad21 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003217 3217 GSM1010848 Myers HudsonAlpha SL13067 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Rad21V0422111PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 RAD21 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Rad21V0422111PkRep1 HCT RAD21 V11 1 Rad21 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003217 3217 GSM1010848 Myers HudsonAlpha SL12230 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Rad21V0422111PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 RAD21 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Pol24h8V0416101PkRep2 HCT Pol2-4H8 V101 2 Pol2-4H8 HCT-116 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001627 1627 GSM803474 Myers HudsonAlpha SL3830 v041610.1 2 exp MACS wgEncodeHaibTfbsHct116Pol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HCT-116 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Pol24h8V0416101PkRep1 HCT Pol2-4H8 V101 1 Pol2-4H8 HCT-116 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001627 1627 GSM803474 Myers HudsonAlpha SL3456 v041610.1 1 exp MACS wgEncodeHaibTfbsHct116Pol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HCT-116 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116NrsfV0422111PkRep2 HCT NRSF V11 2 NRSF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003308 3308 GSM1010869 Myers HudsonAlpha SL14560 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116NrsfV0422111PkRep2 None Peaks Neuron-restrictive silencer transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 NRSF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116NrsfV0422111PkRep1 HCT NRSF V11 1 NRSF HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003308 3308 GSM1010869 Myers HudsonAlpha SL16310 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116NrsfV0422111PkRep1 None Peaks Neuron-restrictive silencer transcription factor colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 NRSF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116MaxV0422111PkRep2 HCT Max V11 2 Max HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003223 3223 GSM1010904 Myers HudsonAlpha SL13075 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116MaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116MaxV0422111PkRep1 HCT Max V11 1 Max HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEH003223 3223 GSM1010904 Myers HudsonAlpha SL12243 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116MaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116JundV0422111PkRep2 HCT JunD V11 2 JunD HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003216 3216 GSM1010847 Myers HudsonAlpha SL13069 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116JundV0422111PkRep2 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 JunD v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116JundV0422111PkRep1 HCT JunD V11 1 JunD HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003216 3216 GSM1010847 Myers HudsonAlpha SL12233 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116JundV0422111PkRep1 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 JunD v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Fosl1V0422111PkRep2 HCT FOSL1 V11 2 FOSL1_(SC-183) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003246 3246 GSM1010756 Myers HudsonAlpha SL13068 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Fosl1V0422111PkRep2 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 FOSL1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Fosl1V0422111PkRep1 HCT FOSL1 V11 1 FOSL1_(SC-183) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003246 3246 GSM1010756 Myers HudsonAlpha SL12231 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Fosl1V0422111PkRep1 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 FOSL1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Elf1V0422111PkRep2 HCT ELF1 V11 2 ELF1_(SC-631) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003307 3307 GSM1010765 Myers HudsonAlpha SL13733 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Elf1V0422111PkRep2 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 ELF1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Elf1V0422111PkRep1 HCT ELF1 V11 1 ELF1_(SC-631) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003307 3307 GSM1010765 Myers HudsonAlpha SL14719 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Elf1V0422111PkRep1 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 ELF1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Egr1V0422111PkRep2 HCT Egr-1 V11 2 Egr-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003215 3215 GSM1010846 Myers HudsonAlpha SL13065 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Egr1V0422111PkRep2 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 Egr-1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Egr1V0422111PkRep1 HCT Egr-1 V11 1 Egr-1 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-15 2013-03-15 wgEncodeEH003215 3215 GSM1010846 Myers HudsonAlpha SL12228 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Egr1V0422111PkRep1 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 Egr-1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116CtcfcV0422111PkRep2 HCT CTCF V11 2 CTCF_(SC-5916) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003220 3220 GSM1010903 Myers HudsonAlpha SL13074 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116CtcfcV0422111PkRep2 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 CTCF 5916 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116CtcfcV0422111PkRep1 HCT CTCF V11 1 CTCF_(SC-5916) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003220 3220 GSM1010903 Myers HudsonAlpha SL12242 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116CtcfcV0422111PkRep1 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 CTCF 5916 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cebpbsc150V0422111PkRep2 HCT CEBPB V11 2 CEBPB_(SC-150) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003219 3219 GSM1010852 Myers HudsonAlpha SL13073 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Cebpbsc150V0422111PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 CEBPB v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cebpbsc150V0422111PkRep1 HCT CEBPB V11 1 CEBPB_(SC-150) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEH003219 3219 GSM1010852 Myers HudsonAlpha SL12240 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Cebpbsc150V0422111PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 CEBPB v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cbx3sc101004V0422111PkRep2 HCT CBX3 V11 2 CBX3_(SC-101004) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003277 3277 GSM1010758 Myers HudsonAlpha SL13066 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Cbx3sc101004V0422111PkRep2 None Peaks At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 CBX3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Cbx3sc101004V0422111PkRep1 HCT CBX3 V11 1 CBX3_(SC-101004) HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003277 3277 GSM1010758 Myers HudsonAlpha SL12229 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Cbx3sc101004V0422111PkRep1 None Peaks At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 CBX3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Atf3V0422111PkRep2 HCT ATF3 V11 2 ATF3 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003276 3276 GSM1010757 Myers HudsonAlpha SL16874 v042211.1 2 exp MACS wgEncodeHaibTfbsHct116Atf3V0422111PkRep2 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 ATF3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHct116Atf3V0422111PkRep1 HCT ATF3 V11 1 ATF3 HCT-116 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003276 3276 GSM1010757 Myers HudsonAlpha SL12234 v042211.1 1 exp MACS wgEncodeHaibTfbsHct116Atf3V0422111PkRep1 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. colorectal carcinoma (PMID: 7214343) Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HCT-116 ATF3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Yy1V0416101PkRep2 GM92 YY1 V101 2 YY1 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001609 1609 GSM803516 Myers HudsonAlpha SL3584 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12892Yy1V0416101PkRep2 None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 YY1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Yy1V0416101PkRep1 GM92 YY1 V101 1 YY1 GM12892 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001609 1609 GSM803516 Myers HudsonAlpha SL2132 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12892Yy1V0416101PkRep1 None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 YY1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Taf1V0416102PkRep2 GM92 TAF1 V102 2 TAF1 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001513 1513 GSM803489 Myers HudsonAlpha SL945 v041610.2 2 exp wgEncodeHaibTfbsGm12892Taf1V0416102PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 TAF1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Taf1V0416102PkRep1 GM92 TAF1 V102 1 TAF1 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001513 1513 GSM803489 Myers HudsonAlpha SL736 v041610.2 1 exp wgEncodeHaibTfbsGm12892Taf1V0416102PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 TAF1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol24h8V0416102PkRep2 GM92 Pol2-4H8 V102 2 Pol2-4H8 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001512 1512 GSM803490 Myers HudsonAlpha SL946 v041610.2 2 exp wgEncodeHaibTfbsGm12892Pol24h8V0416102PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 Pol2-4H8 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol24h8V0416102PkRep1 GM92 Pol2-4H8 V102 1 Pol2-4H8 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001512 1512 GSM803490 Myers HudsonAlpha SL911 v041610.2 1 exp wgEncodeHaibTfbsGm12892Pol24h8V0416102PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 Pol2-4H8 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol2V0416102PkRep2 GM92 Pol2 V102 2 Pol2 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001511 1511 GSM803487 Myers HudsonAlpha SL944 v041610.2 2 exp wgEncodeHaibTfbsGm12892Pol2V0416102PkRep2 None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 Pol2 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pol2V0416102PkRep1 GM92 Pol2 V102 1 Pol2 GM12892 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001511 1511 GSM803487 Myers HudsonAlpha SL909 v041610.2 1 exp wgEncodeHaibTfbsGm12892Pol2V0416102PkRep1 None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 Pol2 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pax5c20V0416101PkRep2 GM92 PAX5 V101 2 PAX5-C20 GM12892 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2011-03-17 wgEncodeEH001546 1546 GSM803334 Myers HudsonAlpha SL2133 hg19 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12892Pax5c20V0416101PkRep2 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 PAX5-C20 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12892Pax5c20V0416101PkRep1 GM92 PAX5 V101 1 PAX5-C20 GM12892 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2011-03-17 wgEncodeEH001546 1546 GSM803334 Myers HudsonAlpha SL1664 hg19 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12892Pax5c20V0416101PkRep1 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12892 PAX5-C20 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Yy1sc281V0416101PkRep2 GM91 YY1 V101 2 YY1_(SC-281) GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-09-27 2011-06-27 wgEncodeEH001573 1573 GSM803535 Myers HudsonAlpha SL2130 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12891Yy1sc281V0416101PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 YY1 281 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Yy1sc281V0416101PkRep1 GM91 YY1 V101 1 YY1_(SC-281) GM12891 ChipSeq ENCODE Jan 2011 Freeze 2010-09-27 2011-06-27 wgEncodeEH001573 1573 GSM803535 Myers HudsonAlpha SL2388 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12891Yy1sc281V0416101PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 YY1 281 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Taf1Pcr1xPkRep2 GM91 TAF1 PCR1 2 TAF1 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001524 1524 GSM803393 Myers HudsonAlpha SL920 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12891Taf1Pcr1xPkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 TAF1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Taf1Pcr1xPkRep1 GM91 TAF1 PCR1 1 TAF1 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001524 1524 GSM803393 Myers HudsonAlpha SL749 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12891Taf1Pcr1xPkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 TAF1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pu1Pcr1xPkRep2 GM91 PU.1 PCR1 2 PU.1 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-10 wgEncodeEH001521 1521 GSM803398 Myers HudsonAlpha SL948 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12891Pu1Pcr1xPkRep2 None Peaks PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 PU.1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pu1Pcr1xPkRep1 GM91 PU.1 PCR1 1 PU.1 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-10 wgEncodeEH001521 1521 GSM803398 Myers HudsonAlpha SL977 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12891Pu1Pcr1xPkRep1 None Peaks PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 PU.1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pou2f2Pcr1xPkRep2 GM91 POU2F2 2 POU2F2 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001520 1520 GSM803397 Myers HudsonAlpha SL918 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12891Pou2f2Pcr1xPkRep2 None Peaks Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 POU2F2 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pou2f2Pcr1xPkRep1 GM91 POU2F2 1 POU2F2 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001520 1520 GSM803397 Myers HudsonAlpha SL802 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12891Pou2f2Pcr1xPkRep1 None Peaks Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 POU2F2 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol24h8Pcr1xPkRep2 GM91 Pol2-4H8 PCR1 2 Pol2-4H8 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001523 1523 GSM803400 Myers HudsonAlpha SL922 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12891Pol24h8Pcr1xPkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 Pol2-4H8 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol24h8Pcr1xPkRep1 GM91 Pol2-4H8 PCR1 1 Pol2-4H8 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001523 1523 GSM803400 Myers HudsonAlpha SL910 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12891Pol24h8Pcr1xPkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 Pol2-4H8 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol2Pcr1xPkRep2 GM91 Pol2 PCR1 2 Pol2 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001522 1522 GSM803399 Myers HudsonAlpha SL921 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12891Pol2Pcr1xPkRep2 None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 Pol2 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pol2Pcr1xPkRep1 GM91 Pol2 PCR1 1 Pol2 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-11 2010-10-11 wgEncodeEH001522 1522 GSM803399 Myers HudsonAlpha SL908 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12891Pol2Pcr1xPkRep1 None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 Pol2 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pax5c20V0416101PkRep2 GM91 PAX5 V101 2 PAX5-C20 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2011-03-17 wgEncodeEH001545 1545 GSM803337 Myers HudsonAlpha SL2131 hg19 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12891Pax5c20V0416101PkRep2 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 PAX5-C20 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12891Pax5c20V0416101PkRep1 GM91 PAX5 V101 1 PAX5-C20 GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2011-03-17 wgEncodeEH001545 1545 GSM803337 Myers HudsonAlpha SL1662 hg19 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12891Pax5c20V0416101PkRep1 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12891 PAX5-C20 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Zbtb7aV0422111PkRep2 ECC1 ZBTB7A 2 ZBTB7A_(SC-34508) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003241 3241 GSM1010752 Myers HudsonAlpha SL14586 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Zbtb7aV0422111PkRep2 None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 ZBTB7A v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Zbtb7aV0422111PkRep1 ECC1 ZBTB7A 1 ZBTB7A_(SC-34508) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003241 3241 GSM1010752 Myers HudsonAlpha SL13275 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Zbtb7aV0422111PkRep1 None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 ZBTB7A v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Yy1sc281V0422111PkRep2 ECC1 YY1 V11 2 YY1_(SC-281) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003240 3240 GSM1010753 Myers HudsonAlpha SL14584 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Yy1sc281V0422111PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 YY1 281 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Yy1sc281V0422111PkRep1 ECC1 YY1 V11 1 YY1_(SC-281) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003240 3240 GSM1010753 Myers HudsonAlpha SL13273 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Yy1sc281V0422111PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 YY1 281 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Usf1V0422111PkRep2 ECC1 USF1 V11 2 USF-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003239 3239 GSM1010886 Myers HudsonAlpha SL14589 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Usf1V0422111PkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 USF-1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Usf1V0422111PkRep1 ECC1 USF1 V11 1 USF-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003239 3239 GSM1010886 Myers HudsonAlpha SL13279 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Usf1V0422111PkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 USF-1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tead4sc101184V0422111PkRep2 ECC1 TEAD4 V11 2 TEAD4_(SC-101184) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003238 3238 GSM1010885 Myers HudsonAlpha SL14591 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Tead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tead4sc101184V0422111PkRep1 ECC1 TEAD4 V11 1 TEAD4_(SC-101184) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003238 3238 GSM1010885 Myers HudsonAlpha SL13281 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Tead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tcf12V0422111PkRep2 ECC1 TCF12 V11 2 TCF12 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003291 3291 GSM1010842 Myers HudsonAlpha SL14063 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Tcf12V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 TCF12 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Tcf12V0422111PkRep1 ECC1 TCF12 V11 1 TCF12 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003291 3291 GSM1010842 Myers HudsonAlpha SL16025 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Tcf12V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 TCF12 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Taf1V0422111PkRep2 ECC1 TAF1 V11 2 TAF1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003256 3256 GSM1010733 Myers HudsonAlpha SL14721 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Taf1V0422111PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 TAF1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Taf1V0422111PkRep1 ECC1 TAF1 V11 1 TAF1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003256 3256 GSM1010733 Myers HudsonAlpha SL13751 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Taf1V0422111PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 TAF1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1SrfV0422111PkRep2 ECC1 SRF V11 2 SRF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003245 3245 GSM1010762 Myers HudsonAlpha SL14583 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1SrfV0422111PkRep2 None Peaks Serum response transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 SRF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1SrfV0422111PkRep1 ECC1 SRF V11 1 SRF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003245 3245 GSM1010762 Myers HudsonAlpha SL13272 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1SrfV0422111PkRep1 None Peaks Serum response transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 SRF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Rad21V0422111PkRep2 ECC1 RAD21 V11 2 Rad21 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003263 3263 GSM1010801 Myers HudsonAlpha SL16305 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Rad21V0422111PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 RAD21 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Rad21V0422111PkRep1 ECC1 RAD21 V11 1 Rad21 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003263 3263 GSM1010801 Myers HudsonAlpha SL13270 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Rad21V0422111PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 RAD21 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hPkRep2 ECC1 Pol2 DMSO 2 Pol2 ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-09-27 2011-06-27 wgEncodeEH001572 1572 GSM803536 Myers HudsonAlpha SL2085 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks RNA Polymerase II epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 Pol2 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hPkRep1 ECC1 Pol2 DMSO 1 Pol2 ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-09-27 2011-06-27 wgEncodeEH001572 1572 GSM803536 Myers HudsonAlpha SL1176 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks RNA Polymerase II epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 Pol2 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1P300V0422111PkRep2 ECC1 p300 V11 2 p300 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003274 3274 GSM1010759 Myers HudsonAlpha SL14585 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1P300V0422111PkRep2 None Peaks EP300(c-20) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 p300 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1P300V0422111PkRep1 ECC1 p300 V11 1 p300 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003274 3274 GSM1010759 Myers HudsonAlpha SL13274 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1P300V0422111PkRep1 None Peaks EP300(c-20) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 p300 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1NrsfV0422111PkRep2 ECC1 NRSF V11 2 NRSF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003290 3290 GSM1010841 Myers HudsonAlpha SL14057 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1NrsfV0422111PkRep2 None Peaks Neuron-restrictive silencer transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 NRSF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1NrsfV0422111PkRep1 ECC1 NRSF V11 1 NRSF ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003290 3290 GSM1010841 Myers HudsonAlpha SL16023 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1NrsfV0422111PkRep1 None Peaks Neuron-restrictive silencer transcription factor epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 NRSF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Nficsc81335V0422111PkRep2 ECC1 NFIC V11 2 NFIC_(SC-81335) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003289 3289 GSM1010855 Myers HudsonAlpha SL16022 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Nficsc81335V0422111PkRep2 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 NFIC v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Nficsc81335V0422111PkRep1 ECC1 NFIC V11 1 NFIC_(SC-81335) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003289 3289 GSM1010855 Myers HudsonAlpha SL14056 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Nficsc81335V0422111PkRep1 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 NFIC v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1MaxV0422111PkRep2 ECC1 Max V11 2 Max ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003268 3268 GSM1010807 Myers HudsonAlpha SL16021 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1MaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1MaxV0422111PkRep1 ECC1 Max V11 1 Max ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003268 3268 GSM1010807 Myers HudsonAlpha SL14054 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1MaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1GrV0416102Dex100nmPkRep2 ECC1 GR DEX PC2 2 GR ECC-1 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2011-03-07 wgEncodeEH001540 1540 GSM803340 Myers HudsonAlpha SL1088 hg19 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1GrV0416102Dex100nmPkRep2 DEX_100nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment ECC-1 GR DEX 100nM PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1GrV0416102Dex100nmPkRep1 ECC1 GR DEX PC2 1 GR ECC-1 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2011-03-07 wgEncodeEH001540 1540 GSM803340 Myers HudsonAlpha SL1012 hg19 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1GrV0416102Dex100nmPkRep1 DEX_100nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment ECC-1 GR DEX 100nM PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxm1sc502V0422111PkRep2 ECC1 FOXM1 V11 2 FOXM1_(SC-502) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003288 3288 GSM1010856 Myers HudsonAlpha SL14725 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Foxm1sc502V0422111PkRep2 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 FOXM1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxm1sc502V0422111PkRep1 ECC1 FOXM1 V11 1 FOXM1_(SC-502) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003288 3288 GSM1010856 Myers HudsonAlpha SL14051 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Foxm1sc502V0422111PkRep1 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 FOXM1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hPkRep2 ECC1 FOXA1 DMSO 2 FOXA1_(SC-6553) ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001586 1586 GSM803444 Myers HudsonAlpha SL2080 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 FOXA1 6553 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hPkRep1 ECC1 FOXA1 DMSO 1 FOXA1_(SC-6553) ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-11-15 2011-08-15 wgEncodeEH001586 1586 GSM803444 Myers HudsonAlpha SL1880 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 FOXA1 6553 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hPkRep2 ECC1 ERa Geni 2 ERalpha_a ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-09-28 2011-06-28 wgEncodeEH001575 1575 GSM803541 Myers HudsonAlpha SL1122 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hPkRep2 Genistein_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Regions of enriched signal in experiment ECC-1 ERa a Genistein v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hPkRep1 ECC1 ERa Geni 1 ERalpha_a ECC-1 ChipSeq ENCODE Jan 2011 Freeze 2010-09-28 2011-06-28 wgEncodeEH001575 1575 GSM803541 Myers HudsonAlpha SL1049 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hPkRep1 Genistein_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Genistein (Myers) Regions of enriched signal in experiment ECC-1 ERa a Genistein v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hPkRep2 ECC1 ERa Estra 2 ERalpha_a ECC-1 ChipSeq ENCODE June 2010 Freeze 2010-05-27 2011-02-27 wgEncodeEH001536 1536 GSM803422 Myers HudsonAlpha SL1093 hg19 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hPkRep2 Estradiol_10nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Regions of enriched signal in experiment ECC-1 ERa a Estradiol v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hPkRep1 ECC1 ERa Estra 1 ERalpha_a ECC-1 ChipSeq ENCODE June 2010 Freeze 2010-05-27 2011-02-27 wgEncodeEH001536 1536 GSM803422 Myers HudsonAlpha SL1011 hg19 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1EralphaaV0416102Est10nm1hPkRep1 Estradiol_10nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 10 nM Estradiol (Myers) Regions of enriched signal in experiment ECC-1 ERa a Estradiol v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hPkRep2 ECC1 ERa BPA 2 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002313 2313 GSM1010747 Myers HudsonAlpha SL2082 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hPkRep2 BPA_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Regions of enriched signal in experiment ECC-1 ERa a BPA v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hPkRep1 ECC1 ERa BPA 1 ERalpha_a ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002313 2313 GSM1010747 Myers HudsonAlpha SL1050 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1EraaV0416102Bpa1hPkRep1 BPA_100nM Peaks This gene encodes an estrogen receptor, a ligand-activated transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcription. The protein localizes to the nucleus where it may form a homodimer or a heterodimer with estrogen receptor 2. Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues such as bone. Estrogen receptors are also involved in pathological processes including breast cancer, endometrial cancer, and osteoporosis. Alternative splicing results in several transcript variants, which differ in their 5-prime UTRs and use different promoters. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Bisphenol A (Myers) Regions of enriched signal in experiment ECC-1 ERa a BPA v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Egr1V0422111PkRep2 ECC1 Egr-1 V11 2 Egr-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003232 3232 GSM1010888 Myers HudsonAlpha SL14590 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Egr1V0422111PkRep2 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 Egr-1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Egr1V0422111PkRep1 ECC1 Egr-1 V11 1 Egr-1 ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003232 3232 GSM1010888 Myers HudsonAlpha SL13280 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Egr1V0422111PkRep1 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 Egr-1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hPkRep2 ECC1 CTCF DMSO 2 CTCF_(SC-5916) ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002300 2300 GSM1010774 Myers HudsonAlpha SL3447 v041610.2 2 exp MACS wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hPkRep2 DMSO_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 CTCF 5916 DMSO v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hPkRep1 ECC1 CTCF DMSO 1 CTCF_(SC-5916) ECC-1 ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002300 2300 GSM1010774 Myers HudsonAlpha SL2630 v041610.2 1 exp MACS wgEncodeHaibTfbsEcc1CtcfcV0416102Dm002p1hPkRep1 DMSO_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Dimethyl sufloxide (DMSO) (Myers) Regions of enriched signal in experiment ECC-1 CTCF 5916 DMSO v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Creb1sc240V0422111PkRep2 ECC1 CREB1 V11 2 CREB1_(SC-240) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003287 3287 GSM1010857 Myers HudsonAlpha SL14723 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Creb1sc240V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 CREB1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Creb1sc240V0422111PkRep1 ECC1 CREB1 V11 1 CREB1_(SC-240) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003287 3287 GSM1010857 Myers HudsonAlpha SL14048 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Creb1sc240V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 CREB1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Cebpbsc150V0422111PkRep2 ECC1 CEBPB V11 2 CEBPB_(SC-150) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003262 3262 GSM1010802 Myers HudsonAlpha SL16302 v042211.1 2 exp MACS wgEncodeHaibTfbsEcc1Cebpbsc150V0422111PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 CEBPB v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsEcc1Cebpbsc150V0422111PkRep1 ECC1 CEBPB V11 1 CEBPB_(SC-150) ECC-1 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003262 3262 GSM1010802 Myers HudsonAlpha SL13276 v042211.1 1 exp MACS wgEncodeHaibTfbsEcc1Cebpbsc150V0422111PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment ECC-1 CEBPB v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshZbtb33V0422111PkRep2 SKSH ZBTB33 V11 2 ZBTB33 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003261 3261 GSM1010799 Myers HudsonAlpha SL14711 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshZbtb33V0422111PkRep2 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH ZBTB33 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshZbtb33V0422111PkRep1 SKSH ZBTB33 V11 1 ZBTB33 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003261 3261 GSM1010799 Myers HudsonAlpha SL13502 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshZbtb33V0422111PkRep1 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH ZBTB33 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshYy1sc281V0422111PkRep2 SKSH YY1 V11 2 YY1_(SC-281) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003228 3228 GSM1010897 Myers HudsonAlpha SL14045 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshYy1sc281V0422111PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH YY1 281 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshYy1sc281V0422111PkRep1 SKSH YY1 V11 1 YY1_(SC-281) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003228 3228 GSM1010897 Myers HudsonAlpha SL13085 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshYy1sc281V0422111PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH YY1 281 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshUsf1V0422111PkRep2 SKSH USF1 V11 2 USF-1 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003269 3269 GSM1010806 Myers HudsonAlpha SL14597 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshUsf1V0422111PkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH USF-1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshUsf1V0422111PkRep1 SKSH USF1 V11 1 USF-1 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003269 3269 GSM1010806 Myers HudsonAlpha SL13084 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshUsf1V0422111PkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH USF-1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTead4sc101184V0422111PkRep2 SKSH TEAD4 V11 2 TEAD4_(SC-101184) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003286 3286 GSM1010858 Myers HudsonAlpha SL14710 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshTead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTead4sc101184V0422111PkRep1 SKSH TEAD4 V11 1 TEAD4_(SC-101184) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003286 3286 GSM1010858 Myers HudsonAlpha SL13501 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshTead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTcf12V0422111PkRep2 SKSH TCF12 V11 2 TCF12 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003227 3227 GSM1010900 Myers HudsonAlpha SL14046 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshTcf12V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH TCF12 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTcf12V0422111PkRep1 SKSH TCF12 V11 1 TCF12 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003227 3227 GSM1010900 Myers HudsonAlpha SL13086 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshTcf12V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH TCF12 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTaf1V0416101PkRep2 SKSH TAF1 V101 2 TAF1 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002301 2301 GSM1010773 Myers HudsonAlpha SL6462 v041610.1 2 exp MACS wgEncodeHaibTfbsSknshTaf1V0416101PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH TAF1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshTaf1V0416101PkRep1 SKSH TAF1 V101 1 TAF1 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-09-05 2012-06-05 wgEncodeEH002301 2301 GSM1010773 Myers HudsonAlpha SL5612 v041610.1 1 exp MACS wgEncodeHaibTfbsSknshTaf1V0416101PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH TAF1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshSin3ak20V0416101PkRep2 SKSH Sin3A V101 2 Sin3Ak-20 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002271 2271 GSM1010816 Myers HudsonAlpha SL5895 v041610.1 2 exp MACS wgEncodeHaibTfbsSknshSin3ak20V0416101PkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshSin3ak20V0416101PkRep1 SKSH Sin3A V101 1 Sin3Ak-20 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002271 2271 GSM1010816 Myers HudsonAlpha SL5043 v041610.1 1 exp MACS wgEncodeHaibTfbsSknshSin3ak20V0416101PkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxraV0422111PkRep2 SKSH RXRA V11 2 RXRA SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003302 3302 GSM1010767 Myers HudsonAlpha SL14708 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshRxraV0422111PkRep2 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH RXRA v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshRxraV0422111PkRep1 SKSH RXRA V11 1 RXRA SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003302 3302 GSM1010767 Myers HudsonAlpha SL13497 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshRxraV0422111PkRep1 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH RXRA v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPol24h8V0416101PkRep2 SKSH Pol2-4H8 V101 2 Pol2-4H8 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002270 2270 GSM1010817 Myers HudsonAlpha SL5607 v041610.1 2 exp MACS wgEncodeHaibTfbsSknshPol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPol24h8V0416101PkRep1 SKSH Pol2-4H8 V101 1 Pol2-4H8 SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002270 2270 GSM1010817 Myers HudsonAlpha SL3768 v041610.1 1 exp MACS wgEncodeHaibTfbsSknshPol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPbx3V0422111PkRep2 SKSH PBx3 V11 2 Pbx3 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003300 3300 GSM1010887 Myers HudsonAlpha SL16042 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshPbx3V0422111PkRep2 None Peaks Pbx 3 (D-17) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH PBx3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshPbx3V0422111PkRep1 SKSH PBx3 V11 1 Pbx3 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003300 3300 GSM1010887 Myers HudsonAlpha SL13495 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshPbx3V0422111PkRep1 None Peaks Pbx 3 (D-17) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH PBx3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshP300V0422111PkRep2 SKSH p300 V11 2 p300 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003270 3270 GSM1010763 Myers HudsonAlpha SL14705 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshP300V0422111PkRep2 None Peaks EP300(c-20) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH p300 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshP300V0422111PkRep1 SKSH p300 V11 1 p300 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEH003270 3270 GSM1010763 Myers HudsonAlpha SL13494 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshP300V0422111PkRep1 None Peaks EP300(c-20) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH p300 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfV0416101PkRep2 SKSH NRSF V101 2 NRSF SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002269 2269 GSM1010735 Myers HudsonAlpha SL5896 v041610.1 2 exp MACS wgEncodeHaibTfbsSknshNrsfV0416101PkRep2 None Peaks Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH NRSF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfV0416101PkRep1 SKSH NRSF V101 1 NRSF SK-N-SH ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002269 2269 GSM1010735 Myers HudsonAlpha SL5494 v041610.1 1 exp MACS wgEncodeHaibTfbsSknshNrsfV0416101PkRep1 None Peaks Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment SK-N-SH NRSF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfPcr2xPkRep2 SKSH NRSF PCR2 2 NRSF SK-N-SH ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001547 1547 GSM803335 Myers HudsonAlpha SL409 PCR2x 2 exp MACS wgEncodeHaibTfbsSknshNrsfPcr2xPkRep2 None Peaks Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment SK-N-SH NRSF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNrsfPcr2xPkRep1 SKSH NRSF PCR2 1 NRSF SK-N-SH ChipSeq ENCODE Jan 2011 Freeze 2010-08-06 2011-05-06 wgEncodeEH001547 1547 GSM803335 Myers HudsonAlpha SL83 PCR2x 1 exp MACS wgEncodeHaibTfbsSknshNrsfPcr2xPkRep1 None Peaks Neuron-restrictive silencer transcription factor neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment SK-N-SH NRSF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNficsc81335V0422111PkRep2 SKSH NFIC V11 2 NFIC_(SC-81335) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-18 wgEncodeEH003237 3237 GSM1010880 Myers HudsonAlpha SL14603 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshNficsc81335V0422111PkRep2 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH NFIC v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshNficsc81335V0422111PkRep1 SKSH NFIC V11 1 NFIC_(SC-81335) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-18 wgEncodeEH003237 3237 GSM1010880 Myers HudsonAlpha SL13313 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshNficsc81335V0422111PkRep1 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH NFIC v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMef2aV0422111PkRep2 SKSH MEF2A V11 2 MEF2A SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003298 3298 GSM1010834 Myers HudsonAlpha SL14704 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshMef2aV0422111PkRep2 None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH MEF2A v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMef2aV0422111PkRep1 SKSH MEF2A V11 1 MEF2A SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003298 3298 GSM1010834 Myers HudsonAlpha SL13493 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshMef2aV0422111PkRep1 None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH MEF2A v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMaxV0422111PkRep2 SKSH Max V11 2 Max SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003299 3299 GSM1010835 Myers HudsonAlpha SL16738 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshMaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshMaxV0422111PkRep1 SKSH Max V11 1 Max SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003299 3299 GSM1010835 Myers HudsonAlpha SL14602 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshMaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshJundV0422111PkRep2 SKSH JunD V11 2 JunD SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003226 3226 GSM1010901 Myers HudsonAlpha SL14042 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshJundV0422111PkRep2 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH JunD v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshJundV0422111PkRep1 SKSH JunD V11 1 JunD SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003226 3226 GSM1010901 Myers HudsonAlpha SL13079 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshJundV0422111PkRep1 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH JunD v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGata3V0422111PkRep2 SKSH GATA3 V11 2 GATA3_(SC-268) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003249 3249 GSM1010738 Myers HudsonAlpha SL14041 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshGata3V0422111PkRep2 None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH GATA3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGata3V0422111PkRep1 SKSH GATA3 V11 1 GATA3_(SC-268) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003249 3249 GSM1010738 Myers HudsonAlpha SL13078 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshGata3V0422111PkRep1 None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH GATA3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGabpV0422111PkRep2 SKSH GABP V11 2 GABP SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003248 3248 GSM1010739 Myers HudsonAlpha SL13752 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshGabpV0422111PkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH GABP v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshGabpV0422111PkRep1 SKSH GABP V11 1 GABP SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003248 3248 GSM1010739 Myers HudsonAlpha SL12627 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshGabpV0422111PkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH GABP v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFoxm1sc502V0422111PkRep2 SKSH FOXM1 V11 2 FOXM1_(SC-502) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003243 3243 GSM1010750 Myers HudsonAlpha SL14596 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshFoxm1sc502V0422111PkRep2 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH FOXM1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFoxm1sc502V0422111PkRep1 SKSH FOXM1 V11 1 FOXM1_(SC-502) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003243 3243 GSM1010750 Myers HudsonAlpha SL13083 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshFoxm1sc502V0422111PkRep1 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH FOXM1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFosl2V0422111PkRep2 SKSH FOSL2 V11 2 FOSL2 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003297 3297 GSM1010840 Myers HudsonAlpha SL16737 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshFosl2V0422111PkRep2 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH FOSL2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshFosl2V0422111PkRep1 SKSH FOSL2 V11 1 FOSL2 SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003297 3297 GSM1010840 Myers HudsonAlpha SL13310 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshFosl2V0422111PkRep1 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH FOSL2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshElf1V0422111PkRep2 SKSH ELF1 V11 2 ELF1_(SC-631) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003242 3242 GSM1010751 Myers HudsonAlpha SL14600 v042211.1 2 exp MACS wgEncodeHaibTfbsSknshElf1V0422111PkRep2 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH ELF1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsSknshElf1V0422111PkRep1 SKSH ELF1 V11 1 ELF1_(SC-631) SK-N-SH ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003242 3242 GSM1010751 Myers HudsonAlpha SL13309 v042211.1 1 exp MACS wgEncodeHaibTfbsSknshElf1V0422111PkRep1 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment SK-N-SH ELF1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tead4sc101184V0422111PkRep2 MCF-7 TEAD4 V11 2 TEAD4_(SC-101184) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003284 3284 GSM1010860 Myers HudsonAlpha SL16341 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Tead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tead4sc101184V0422111PkRep1 MCF-7 TEAD4 V11 1 TEAD4_(SC-101184) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003284 3284 GSM1010860 Myers HudsonAlpha SL14575 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Tead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tcf12V0422111PkRep2 MCF-7 TCF12 V11 2 TCF12 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003283 3283 GSM1010861 Myers HudsonAlpha SL16340 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Tcf12V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 TCF12 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Tcf12V0422111PkRep1 MCF-7 TCF12 V11 1 TCF12 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003283 3283 GSM1010861 Myers HudsonAlpha SL14574 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Tcf12V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 TCF12 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Taf1V0422111PkRep2 MCF-7 TAF1 V11 2 TAF1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003317 3317 GSM1010811 Myers HudsonAlpha SL16339 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Taf1V0422111PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 TAF1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Taf1V0422111PkRep1 MCF-7 TAF1 V11 1 TAF1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003317 3317 GSM1010811 Myers HudsonAlpha SL14572 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Taf1V0422111PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 TAF1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7SrfV0422111PkRep2 MCF-7 SRF V11 2 SRF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003296 3296 GSM1010839 Myers HudsonAlpha SL16044 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7SrfV0422111PkRep2 None Peaks Serum response transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 SRF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7SrfV0422111PkRep1 MCF-7 SRF V11 1 SRF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003296 3296 GSM1010839 Myers HudsonAlpha SL13723 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7SrfV0422111PkRep1 None Peaks Serum response transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 SRF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Sin3ak20V0422111PkRep2 MCF-7 Sin3A V11 2 Sin3Ak-20 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003282 3282 GSM1010862 Myers HudsonAlpha SL14716 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Sin3ak20V0422111PkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 Sin3Ak-20 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Sin3ak20V0422111PkRep1 MCF-7 Sin3A V11 1 Sin3Ak-20 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003282 3282 GSM1010862 Myers HudsonAlpha SL13726 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Sin3ak20V0422111PkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 Sin3Ak-20 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Rad21V0422111PkRep2 MCF-7 RAD21 V11 2 Rad21 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003259 3259 GSM1010791 Myers HudsonAlpha SL16336 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Rad21V0422111PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 RAD21 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Rad21V0422111PkRep1 MCF-7 RAD21 V11 1 Rad21 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003259 3259 GSM1010791 Myers HudsonAlpha SL13724 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Rad21V0422111PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 RAD21 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Pmlsc71910V0422111PkRep2 MCF-7 PML V11 2 PML_(SC-71910) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003295 3295 GSM1010838 Myers HudsonAlpha SL16026 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Pmlsc71910V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 PML v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Pmlsc71910V0422111PkRep1 MCF-7 PML V11 1 PML_(SC-71910) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003295 3295 GSM1010838 Myers HudsonAlpha SL13722 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Pmlsc71910V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 PML v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7P300V0422111PkRep2 MCF-7 p300 V11 2 p300 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003260 3260 GSM1010800 Myers HudsonAlpha SL16335 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7P300V0422111PkRep2 None Peaks EP300(c-20) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 p300 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7P300V0422111PkRep1 MCF-7 p300 V11 1 p300 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003260 3260 GSM1010800 Myers HudsonAlpha SL13492 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7P300V0422111PkRep1 None Peaks EP300(c-20) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 p300 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7NrsfV0422111PkRep2 MCF-7 NRSF V11 2 NRSF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003231 3231 GSM1010891 Myers HudsonAlpha SL14698 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7NrsfV0422111PkRep2 None Peaks Neuron-restrictive silencer transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 NRSF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7NrsfV0422111PkRep1 MCF-7 NRSF V11 1 NRSF MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003231 3231 GSM1010891 Myers HudsonAlpha SL13491 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7NrsfV0422111PkRep1 None Peaks Neuron-restrictive silencer transcription factor mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 NRSF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111PkRep2 MCF-7 NR2F2 V11 2 NR2F2_(SC-271940) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003294 3294 GSM1010837 Myers HudsonAlpha SL14697 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111PkRep2 None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 NR2F2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111PkRep1 MCF-7 NR2F2 V11 1 NR2F2_(SC-271940) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003294 3294 GSM1010837 Myers HudsonAlpha SL13490 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111PkRep1 None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 NR2F2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7MaxV0422111PkRep2 MCF-7 Max V11 2 Max MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003281 3281 GSM1010863 Myers HudsonAlpha SL14695 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7MaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7MaxV0422111PkRep1 MCF-7 Max V11 1 Max MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003281 3281 GSM1010863 Myers HudsonAlpha SL13485 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7MaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7JundV0422111PkRep2 MCF-7 JunD V11 2 JunD MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003236 3236 GSM1010892 Myers HudsonAlpha SL14694 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7JundV0422111PkRep2 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 JunD v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7JundV0422111PkRep1 MCF-7 JunD V11 1 JunD MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003236 3236 GSM1010892 Myers HudsonAlpha SL13484 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7JundV0422111PkRep1 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 JunD v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep2 MCF-7 HDAC2 V11 2 HDAC2_(SC-6296) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003258 3258 GSM1010825 Myers HudsonAlpha SL16334 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep2 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 HDAC2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep1 MCF-7 HDAC2 V11 1 HDAC2_(SC-6296) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003258 3258 GSM1010825 Myers HudsonAlpha SL13483 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep1 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 HDAC2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Gata3V0422111PkRep2 MCF-7 GATA3 V11 2 GATA3_(SC-268) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003235 3235 GSM1010783 Myers HudsonAlpha SL14692 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Gata3V0422111PkRep2 None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 GATA3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Gata3V0422111PkRep1 MCF-7 GATA3 V11 1 GATA3_(SC-268) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003235 3235 GSM1010783 Myers HudsonAlpha SL13482 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Gata3V0422111PkRep1 None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 GATA3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7GabpV0422111PkRep2 MCF-7 GABP V11 2 GABP MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003280 3280 GSM1010864 Myers HudsonAlpha SL14683 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7GabpV0422111PkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 GABP v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7GabpV0422111PkRep1 MCF-7 GABP V11 1 GABP MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003280 3280 GSM1010864 Myers HudsonAlpha SL13459 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7GabpV0422111PkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 GABP v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Foxm1sc502V0422111PkRep2 MCF-7 FOXM1 V11 2 FOXM1_(SC-502) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003279 3279 GSM1010769 Myers HudsonAlpha SL14686 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Foxm1sc502V0422111PkRep2 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 FOXM1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Foxm1sc502V0422111PkRep1 MCF-7 FOXM1 V11 1 FOXM1_(SC-502) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003279 3279 GSM1010769 Myers HudsonAlpha SL13462 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Foxm1sc502V0422111PkRep1 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 FOXM1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Fosl2V0422111PkRep2 MCF-7 FOSL2 V11 2 FOSL2 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003278 3278 GSM1010768 Myers HudsonAlpha SL14682 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Fosl2V0422111PkRep2 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 FOSL2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Fosl2V0422111PkRep1 MCF-7 FOSL2 V11 1 FOSL2 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003278 3278 GSM1010768 Myers HudsonAlpha SL13457 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Fosl2V0422111PkRep1 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 FOSL2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Elf1V0422111PkRep2 MCF-7 ELF1 V11 2 ELF1_(SC-631) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003234 3234 GSM1010764 Myers HudsonAlpha SL14690 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Elf1V0422111PkRep2 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 ELF1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Elf1V0422111PkRep1 MCF-7 ELF1 V11 1 ELF1_(SC-631) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003234 3234 GSM1010764 Myers HudsonAlpha SL13466 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Elf1V0422111PkRep1 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 ELF1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Egr1V0422111PkRep2 MCF-7 Egr-1 V11 2 Egr-1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003293 3293 GSM1010844 Myers HudsonAlpha SL14689 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Egr1V0422111PkRep2 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 Egr-1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Egr1V0422111PkRep1 MCF-7 Egr-1 V11 1 Egr-1 MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003293 3293 GSM1010844 Myers HudsonAlpha SL13465 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Egr1V0422111PkRep1 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 Egr-1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7CtcfcV0422111PkRep2 MCF-7 CTCF V11 2 CTCF_(SC-5916) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003257 3257 GSM1010734 Myers HudsonAlpha SL16333 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7CtcfcV0422111PkRep2 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 CTCF 5916 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7CtcfcV0422111PkRep1 MCF-7 CTCF V11 1 CTCF_(SC-5916) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003257 3257 GSM1010734 Myers HudsonAlpha SL13463 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7CtcfcV0422111PkRep1 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 CTCF 5916 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Cebpbsc150V0422111PkRep2 MCF-7 CEBPB V11 2 CEBPB_(SC-150) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003233 3233 GSM1010889 Myers HudsonAlpha SL14684 v042211.1 2 exp MACS wgEncodeHaibTfbsMcf7Cebpbsc150V0422111PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 CEBPB v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsMcf7Cebpbsc150V0422111PkRep1 MCF-7 CEBPB V11 1 CEBPB_(SC-150) MCF-7 ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEH003233 3233 GSM1010889 Myers HudsonAlpha SL13460 v042211.1 1 exp MACS wgEncodeHaibTfbsMcf7Cebpbsc150V0422111PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment MCF-7 CEBPB v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol24h8V0416101PkRep2 HUVEC Pol2-4H8 V101 2 Pol2-4H8 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002298 2298 GSM1010824 Myers HudsonAlpha SL2387 v041610.1 2 exp MACS wgEncodeHaibTfbsHuvecPol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HUVEC Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol24h8V0416101PkRep1 HUVEC Pol2-4H8 V101 1 Pol2-4H8 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002298 2298 GSM1010824 Myers HudsonAlpha SL1104 v041610.1 1 exp MACS wgEncodeHaibTfbsHuvecPol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HUVEC Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol2Pcr1xPkRep2 HUVEC Pol2 PCR1 2 Pol2 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002297 2297 GSM1010830 Myers HudsonAlpha SL6966 PCR1x 2 exp MACS wgEncodeHaibTfbsHuvecPol2Pcr1xPkRep2 None Peaks RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HUVEC Pol2 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHuvecPol2Pcr1xPkRep1 HUVEC Pol2 PCR1 1 Pol2 HUVEC ChipSeq ENCODE Mar 2012 Freeze 2011-09-02 2012-06-02 wgEncodeEH002297 2297 GSM1010830 Myers HudsonAlpha SL1103 PCR1x 1 exp MACS wgEncodeHaibTfbsHuvecPol2Pcr1xPkRep1 None Peaks RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HUVEC Pol2 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zeb1V0422111PkRep2 HepG ZEB1 V11 2 ZEB1_(SC-25388) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003315 3315 GSM1010809 Myers HudsonAlpha SL16318 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Zeb1V0422111PkRep2 None Peaks This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 ZEB1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zeb1V0422111PkRep1 HepG ZEB1 V11 1 ZEB1_(SC-25388) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003315 3315 GSM1010809 Myers HudsonAlpha SL13301 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Zeb1V0422111PkRep1 None Peaks This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 ZEB1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb7aV0416101PkRep2 HepG ZBTB7A 2 ZBTB7A_(SC-34508) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002296 2296 GSM1010831 Myers HudsonAlpha SL6464 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Zbtb7aV0416101PkRep2 None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ZBTB7A v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb7aV0416101PkRep1 HepG ZBTB7A 1 ZBTB7A_(SC-34508) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002296 2296 GSM1010831 Myers HudsonAlpha SL3973 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Zbtb7aV0416101PkRep1 None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ZBTB7A v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33V0416101PkRep2 HepG ZBTB33 2 ZBTB33 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001642 1642 GSM803418 Myers HudsonAlpha SL3987 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Zbtb33V0416101PkRep2 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ZBTB33 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33V0416101PkRep1 HepG ZBTB33 1 ZBTB33 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001642 1642 GSM803418 Myers HudsonAlpha SL3929 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Zbtb33V0416101PkRep1 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ZBTB33 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33Pcr1xPkRep2 HepG ZBTB33 2 ZBTB33 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-12-17 2010-09-16 wgEncodeEH001503 1503 GSM803449 Myers HudsonAlpha SL1055 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHepg2Zbtb33Pcr1xPkRep2 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ZBTB33 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Zbtb33Pcr1xPkRep1 HepG ZBTB33 1 ZBTB33 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-12-17 2010-09-16 wgEncodeEH001503 1503 GSM803449 Myers HudsonAlpha SL981 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHepg2Zbtb33Pcr1xPkRep1 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ZBTB33 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Yy1sc281V0416101PkRep2 HepG YY1 V101 2 YY1_(SC-281) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001661 1661 GSM803381 Myers HudsonAlpha SL3927 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Yy1sc281V0416101PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 YY1 281 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Yy1sc281V0416101PkRep1 HepG YY1 V101 1 YY1_(SC-281) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001661 1661 GSM803381 Myers HudsonAlpha SL2195 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Yy1sc281V0416101PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 YY1 281 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Usf1Pcr1xPkRep2 HepG USF1 PCR1 2 USF-1 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-07-17 2010-04-17 wgEncodeEH001472 1472 GSM803527 Myers HudsonAlpha SL636 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHepg2Usf1Pcr1xPkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 USF-1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Usf1Pcr1xPkRep1 HepG USF1 PCR1 1 USF-1 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-07-17 2010-04-17 wgEncodeEH001472 1472 GSM803527 Myers HudsonAlpha SL582 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHepg2Usf1Pcr1xPkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 USF-1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tead4sc101184V0422111PkRep2 HepG TEAD4 V11 2 TEAD4_(SC-101184) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002345 2345 GSM1010875 Myers HudsonAlpha SL9545 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Tead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tead4sc101184V0422111PkRep1 HepG TEAD4 V11 1 TEAD4_(SC-101184) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002345 2345 GSM1010875 Myers HudsonAlpha SL8584 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Tead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tcf12Pcr1xPkRep2 HepG TCF12 PCR1 2 TCF12 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2011-03-07 wgEncodeEH001544 1544 GSM803336 Myers HudsonAlpha SL1167 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsHepg2Tcf12Pcr1xPkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 TCF12 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Tcf12Pcr1xPkRep1 HepG TCF12 PCR1 1 TCF12 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001544 1544 GSM803336 Myers HudsonAlpha SL1060 PCR1x 1 exp wgEncodeHaibTfbsHepg2Tcf12Pcr1xPkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 TCF12 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Taf1Pcr2xPkRep2 HepG TAF1 PCR2 2 TAF1 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001551 1551 GSM803367 Myers HudsonAlpha SL359 PCR2x 2 exp MACS wgEncodeHaibTfbsHepg2Taf1Pcr2xPkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 TAF1 PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Taf1Pcr2xPkRep1 HepG TAF1 PCR2 1 TAF1 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001551 1551 GSM803367 Myers HudsonAlpha SL358 PCR2x 1 exp MACS wgEncodeHaibTfbsHepg2Taf1Pcr2xPkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 TAF1 PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2SrfV0416101PkRep2 HepG SRF V101 2 SRF HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001611 1611 GSM803502 Myers HudsonAlpha SL3275 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2SrfV0416101PkRep2 None Peaks Serum response transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 SRF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2SrfV0416101PkRep1 HepG SRF V101 1 SRF HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001611 1611 GSM803502 Myers HudsonAlpha SL3156 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2SrfV0416101PkRep1 None Peaks Serum response transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 SRF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp2V0422111PkRep2 HepG SP2 V11 2 SP2_(SC-643) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002264 2264 GSM1010787 Myers HudsonAlpha SL6006 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Sp2V0422111PkRep2 None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 SP2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp2V0422111PkRep1 HepG SP2 V11 1 SP2_(SC-643) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002264 2264 GSM1010787 Myers HudsonAlpha SL5688 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Sp2V0422111PkRep1 None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 SP2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp1Pcr1xPkRep2 HepG SP1 PCR1 2 SP1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-09-13 2011-06-13 wgEncodeEH001561 1561 GSM803507 Myers HudsonAlpha SL1194 PCR1x 2 exp wgEncodeHaibTfbsHepg2Sp1Pcr1xPkRep2 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 SP1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sp1Pcr1xPkRep1 HepG SP1 PCR1 1 SP1 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-09-13 2011-06-13 wgEncodeEH001561 1561 GSM803507 Myers HudsonAlpha SL1056 PCR1x 1 exp wgEncodeHaibTfbsHepg2Sp1Pcr1xPkRep1 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 SP1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xPkRep2 HepG Sin3A PCR1 2 Sin3Ak-20 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-07-17 2010-04-17 wgEncodeEH001471 1471 GSM803530 Myers HudsonAlpha SL637 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xPkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 Sin3Ak-20 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xPkRep1 HepG Sin3A PCR1 1 Sin3Ak-20 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-07-17 2010-04-17 wgEncodeEH001471 1471 GSM803530 Myers HudsonAlpha SL583 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xPkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 Sin3Ak-20 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxraPcr1xPkRep2 HepG RXRA PCR1 2 RXRA HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-12-25 2010-09-25 wgEncodeEH001506 1506 GSM803452 Myers HudsonAlpha SL1054 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHepg2RxraPcr1xPkRep2 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 RXRA PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2RxraPcr1xPkRep1 HepG RXRA PCR1 1 RXRA HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-12-25 2010-09-25 wgEncodeEH001506 1506 GSM803452 Myers HudsonAlpha SL984 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHepg2RxraPcr1xPkRep1 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 RXRA PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Rad21V0416101PkRep2 HepG RAD21 V101 2 Rad21 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001608 1608 GSM803517 Myers HudsonAlpha SL3586 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Rad21V0416101PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 RAD21 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Rad21V0416101PkRep1 HepG RAD21 V101 1 Rad21 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001608 1608 GSM803517 Myers HudsonAlpha SL3179 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Rad21V0416101PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 RAD21 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol24h8V0416102PkRep2 HepG Pol2-4H8 V102 2 Pol2-4H8 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002278 2278 GSM1010821 Myers HudsonAlpha SL5604 v041610.2 2 exp MACS wgEncodeHaibTfbsHepg2Pol24h8V0416102PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 Pol2-4H8 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol24h8V0416102PkRep1 HepG Pol2-4H8 V102 1 Pol2-4H8 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002278 2278 GSM1010821 Myers HudsonAlpha SL1363 v041610.2 1 exp MACS wgEncodeHaibTfbsHepg2Pol24h8V0416102PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 Pol2-4H8 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol2Pcr2xPkRep2 HepG Pol2 PCR2 2 Pol2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001550 1550 GSM803368 Myers HudsonAlpha SL349 PCR2x 2 exp MACS wgEncodeHaibTfbsHepg2Pol2Pcr2xPkRep2 None Peaks RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 Pol2 PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Pol2Pcr2xPkRep1 HepG Pol2 PCR2 1 Pol2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001550 1550 GSM803368 Myers HudsonAlpha SL348 PCR2x 1 exp MACS wgEncodeHaibTfbsHepg2Pol2Pcr2xPkRep1 None Peaks RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 Pol2 PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2P300V0416101PkRep2 HepG p300 V101 2 p300 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001612 1612 GSM803499 Myers HudsonAlpha SL3644 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2P300V0416101PkRep2 None Peaks EP300(c-20) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 p300 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2P300V0416101PkRep1 HepG p300 V101 1 p300 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-15 2011-09-15 wgEncodeEH001612 1612 GSM803499 Myers HudsonAlpha SL3154 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2P300V0416101PkRep1 None Peaks EP300(c-20) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 p300 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfV0416101PkRep2 HepG NRSF V101 2 NRSF HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002263 2263 GSM1010784 Myers HudsonAlpha SL5897 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2NrsfV0416101PkRep2 None Peaks Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 NRSF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfV0416101PkRep1 HepG NRSF V101 1 NRSF HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002263 2263 GSM1010784 Myers HudsonAlpha SL5040 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2NrsfV0416101PkRep1 None Peaks Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 NRSF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep2 HepG NRSF PCR2 2 NRSF HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001549 1549 GSM803344 Myers HudsonAlpha SL274 PCR2x 2 exp MACS wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep2 None Peaks Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 NRSF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep1 HepG NRSF PCR2 1 NRSF HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001549 1549 GSM803344 Myers HudsonAlpha SL273 PCR2x 1 exp MACS wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep1 None Peaks Neuron-restrictive silencer transcription factor hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 NRSF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111PkRep2 HepG NR2F2 V11 2 NR2F2_(SC-271940) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003314 3314 GSM1010810 Myers HudsonAlpha SL16316 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111PkRep2 None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 NR2F2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111PkRep1 HepG NR2F2 V11 1 NR2F2_(SC-271940) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003314 3314 GSM1010810 Myers HudsonAlpha SL12644 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111PkRep1 None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 NR2F2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nficsc81335V0422111PkRep2 HepG NFIC V11 2 NFIC_(SC-81335) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002319 2319 GSM1010741 Myers HudsonAlpha SL7554 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Nficsc81335V0422111PkRep2 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 NFIC v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Nficsc81335V0422111PkRep1 HepG NFIC V11 1 NFIC_(SC-81335) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002319 2319 GSM1010741 Myers HudsonAlpha SL7102 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Nficsc81335V0422111PkRep1 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 NFIC v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111PkRep2 HepG MYBL2 V11 2 MYBL2_(SC-81192) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002344 2344 GSM1010876 Myers HudsonAlpha SL7564 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111PkRep2 None Peaks The protein encoded by this gene, a member of the MYB family of transcription factor genes, is a nuclear protein involved in cell cycle progression. The encoded protein is phosphorylated by cyclin A/cyclin-dependent kinase 2 during the S-phase of the cell cycle and possesses both activator and repressor activities. It has been shown to activate the cell division cycle 2, cyclin D1, and insulin-like growth factor-binding protein 5 genes. Transcript variants may exist for this gene, but their full-length natures have not been determined. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 MYBL2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111PkRep1 HepG MYBL2 V11 1 MYBL2_(SC-81192) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002344 2344 GSM1010876 Myers HudsonAlpha SL7101 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111PkRep1 None Peaks The protein encoded by this gene, a member of the MYB family of transcription factor genes, is a nuclear protein involved in cell cycle progression. The encoded protein is phosphorylated by cyclin A/cyclin-dependent kinase 2 during the S-phase of the cell cycle and possesses both activator and repressor activities. It has been shown to activate the cell division cycle 2, cyclin D1, and insulin-like growth factor-binding protein 5 genes. Transcript variants may exist for this gene, but their full-length natures have not been determined. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 MYBL2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111PkRep2 HepG MBD4 V11 2 MBD4_(SC-271530) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002318 2318 GSM1010740 Myers HudsonAlpha SL8132 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111PkRep2 None Peaks MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein sequence similarity to bacterial DNA repair enzymes and thus may have some function in DNA repair. Further, MBD4 gene mutations are detected in tumors with primary microsatellite-instability (MSI), a form of genomic instability associated with defective DNA mismatch repair, and MBD4 gene meets 4 of 5 criteria of a bona fide MIS target gene. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 MBD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111PkRep1 HepG MBD4 V11 1 MBD4_(SC-271530) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002318 2318 GSM1010740 Myers HudsonAlpha SL7901 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111PkRep1 None Peaks MBD4 may function to mediate the biological consequences of the methylation signal. In addition, MBD4 has protein sequence similarity to bacterial DNA repair enzymes and thus may have some function in DNA repair. Further, MBD4 gene mutations are detected in tumors with primary microsatellite-instability (MSI), a form of genomic instability associated with defective DNA mismatch repair, and MBD4 gene meets 4 of 5 criteria of a bona fide MIS target gene. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 MBD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2MaxV0422111PkRep2 HepG Max V11 2 Max HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003254 3254 GSM1010865 Myers HudsonAlpha SL13292 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2MaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2MaxV0422111PkRep1 HepG Max V11 1 Max HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003254 3254 GSM1010865 Myers HudsonAlpha SL12422 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2MaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2JundPcr1xPkRep2 HepG JunD PCR1 2 JunD HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-07-17 2010-04-17 wgEncodeEH001470 1470 GSM803500 Myers HudsonAlpha SL629 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHepg2JundPcr1xPkRep2 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 JunD PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2JundPcr1xPkRep1 HepG JunD PCR1 1 JunD HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-07-17 2010-04-17 wgEncodeEH001470 1470 GSM803500 Myers HudsonAlpha SL635 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHepg2JundPcr1xPkRep1 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 JunD PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101PkRep2 HepG HNF4G V101 2 HNF4G_(SC-6558) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001651 1651 GSM803404 Myers HudsonAlpha SL3463 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101PkRep2 None Peaks Hepatocyte nuclear factor 4 gamma (HNF4G) also known as NR2A2 (nuclear receptor subfamily 2, group A, member 2) is a nuclear receptor that in humans is encoded by the HNF4G gene hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 HNF4G v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101PkRep1 HepG HNF4G V101 1 HNF4G_(SC-6558) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001651 1651 GSM803404 Myers HudsonAlpha SL3178 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101PkRep1 None Peaks Hepatocyte nuclear factor 4 gamma (HNF4G) also known as NR2A2 (nuclear receptor subfamily 2, group A, member 2) is a nuclear receptor that in humans is encoded by the HNF4G gene hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 HNF4G v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101PkRep2 HepG HNF4A V101 2 HNF4A_(SC-8987) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001595 1595 GSM803460 Myers HudsonAlpha SL2125 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101PkRep2 None Peaks The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 HNF4A v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101PkRep1 HepG HNF4A V101 1 HNF4A_(SC-8987) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001595 1595 GSM803460 Myers HudsonAlpha SL1481 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101PkRep1 None Peaks The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 HNF4A v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101PkRep2 HepG HDAC2 V101 2 HDAC2_(SC-6296) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001618 1618 GSM803493 Myers HudsonAlpha SL3583 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101PkRep2 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 HDAC2 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101PkRep1 HepG HDAC2 V101 1 HDAC2_(SC-6296) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001618 1618 GSM803493 Myers HudsonAlpha SL3177 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101PkRep1 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 HDAC2 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2GabpPcr2xPkRep2 HepG GABP PCR2 2 GABP HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001548 1548 GSM803343 Myers HudsonAlpha SL276 PCR2x 2 exp MACS wgEncodeHaibTfbsHepg2GabpPcr2xPkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 GABP PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2GabpPcr2xPkRep1 HepG GABP PCR2 1 GABP HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2011-03-21 wgEncodeEH001548 1548 GSM803343 Myers HudsonAlpha SL275 PCR2x 1 exp MACS wgEncodeHaibTfbsHepg2GabpPcr2xPkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment HepG2 GABP PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101PkRep2 HepG FOXA2 V101 2 FOXA2_(SC-6554) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001650 1650 GSM803403 Myers HudsonAlpha SL3175 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101PkRep2 None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOXA2 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101PkRep1 HepG FOXA2 V101 1 FOXA2_(SC-6554) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001650 1650 GSM803403 Myers HudsonAlpha SL2196 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101PkRep1 None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOXA2 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101PkRep2 HepG FOXA1 V101 2 FOXA1_(SC-6553) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001594 1594 GSM803461 Myers HudsonAlpha SL2124 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101PkRep2 None Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOXA1 6553 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101PkRep1 HepG FOXA1 V101 1 FOXA1_(SC-6553) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001594 1594 GSM803461 Myers HudsonAlpha SL1786 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101PkRep1 None Peaks This gene encodes a member of the forehead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver (RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOXA1 6553 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101PkRep2 HepG FOXA1 V101 2 FOXA1_(SC-101058) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001630 1630 GSM803432 Myers HudsonAlpha SL2194 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101PkRep2 None Peaks This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOXA1 101058 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101PkRep1 HepG FOXA1 V101 1 FOXA1_(SC-101058) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001630 1630 GSM803432 Myers HudsonAlpha SL1788 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101PkRep1 None Peaks This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOXA1 101058 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Fosl2V0416101PkRep2 HepG FOSL2 V101 2 FOSL2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-06-07 2011-03-07 wgEncodeEH001501 1501 GSM803451 Myers HudsonAlpha SL1107 hg18 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Fosl2V0416101PkRep2 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOSL2 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Fosl2V0416101PkRep1 HepG FOSL2 V101 1 FOSL2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-04 2009-12-22 2010-09-22 wgEncodeEH001501 1501 GSM803451 Myers HudsonAlpha SL632 hg18 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Fosl2V0416101PkRep1 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 FOSL2 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Elf1sc631V0416101PkRep2 HepG ELF1 V101 2 ELF1_(SC-631) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001641 1641 GSM803415 Myers HudsonAlpha SL3986 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Elf1sc631V0416101PkRep2 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ELF1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Elf1sc631V0416101PkRep1 HepG ELF1 V101 1 ELF1_(SC-631) HepG2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001641 1641 GSM803415 Myers HudsonAlpha SL3645 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Elf1sc631V0416101PkRep1 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ELF1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101PkRep2 HepG CTCF V101 2 CTCF_(SC-5916) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2010-01-06 2010-10-06 wgEncodeEH001516 1516 GSM803486 Myers HudsonAlpha SL3582 v041610.1 2 exp wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101PkRep2 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 CTCF 5916 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101PkRep1 HepG CTCF V101 1 CTCF_(SC-5916) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2010-01-06 2010-10-06 wgEncodeEH001516 1516 GSM803486 Myers HudsonAlpha SL3176 v041610.1 1 exp wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101PkRep1 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 CTCF 5916 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Creb1sc240V0422111PkRep2 HepG CREB1 V11 2 CREB1_(SC-240) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003312 3312 GSM1010808 Myers HudsonAlpha SL13290 v042211.1 2 exp MACS wgEncodeHaibTfbsHepg2Creb1sc240V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 CREB1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Creb1sc240V0422111PkRep1 HepG CREB1 V11 1 CREB1_(SC-240) HepG2 ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003312 3312 GSM1010808 Myers HudsonAlpha SL12405 v042211.1 1 exp MACS wgEncodeHaibTfbsHepg2Creb1sc240V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment HepG2 CREB1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpdsc636V0416101PkRep2 HepG CEBPD V101 2 CEBPD_(SC-636) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002305 2305 GSM1010777 Myers HudsonAlpha SL4940 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Cebpdsc636V0416101PkRep2 None Peaks The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 CEBPD v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpdsc636V0416101PkRep1 HepG CEBPD V101 1 CEBPD_(SC-636) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002305 2305 GSM1010777 Myers HudsonAlpha SL4210 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Cebpdsc636V0416101PkRep1 None Peaks The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 CEBPD v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpbsc150V0416101PkRep2 HepG CEBPB V101 2 CEBPB_(SC-150) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002304 2304 GSM1010778 Myers HudsonAlpha SL4939 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Cebpbsc150V0416101PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 CEBPB v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Cebpbsc150V0416101PkRep1 HepG CEBPB V101 1 CEBPB_(SC-150) HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002304 2304 GSM1010778 Myers HudsonAlpha SL4209 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Cebpbsc150V0416101PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 CEBPB v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Bhlhe40V0416101PkRep2 HepG BHLHE40 2 BHLHE40 HepG2 ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001515 1515 GSM803483 Myers HudsonAlpha SL3460 v041610.1 2 exp wgEncodeHaibTfbsHepg2Bhlhe40V0416101PkRep2 None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 BHLHE40 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Bhlhe40V0416101PkRep1 HepG BHLHE40 1 BHLHE40 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-06-07 2011-03-07 wgEncodeEH001515 1515 GSM803483 Myers HudsonAlpha SL1059 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Bhlhe40V0416101PkRep1 None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 BHLHE40 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Atf3V0416101PkRep2 HepG ATF3 V101 2 ATF3 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001568 1568 GSM803503 Myers HudsonAlpha SL1787 v041610.1 2 exp MACS wgEncodeHaibTfbsHepg2Atf3V0416101PkRep2 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ATF3 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHepg2Atf3V0416101PkRep1 HepG ATF3 V101 1 ATF3 HepG2 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001568 1568 GSM803503 Myers HudsonAlpha SL2386 v041610.1 1 exp MACS wgEncodeHaibTfbsHepg2Atf3V0416101PkRep1 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. hepatocellular carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HepG2 ATF3 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Taf1Pcr1xPkRep2 HeLa TAF1 PCR1 2 TAF1 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-18 2010-09-18 wgEncodeEH001505 1505 GSM803455 Myers HudsonAlpha SL706 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHelas3Taf1Pcr1xPkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 TAF1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Taf1Pcr1xPkRep1 HeLa TAF1 PCR1 1 TAF1 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-18 2010-09-18 wgEncodeEH001505 1505 GSM803455 Myers HudsonAlpha SL590 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHelas3Taf1Pcr1xPkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 TAF1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Pol2Pcr1xPkRep2 HeLa Pol2 PCR1 2 Pol2 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2009-07-19 2010-04-19 wgEncodeEH001474 1474 GSM803533 Myers HudsonAlpha SL672 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHelas3Pol2Pcr1xPkRep2 None Peaks RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 Pol2 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3Pol2Pcr1xPkRep1 HeLa Pol2 PCR1 1 Pol2 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-19 2010-04-19 wgEncodeEH001474 1474 GSM803533 Myers HudsonAlpha SL631 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHelas3Pol2Pcr1xPkRep1 None Peaks RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 Pol2 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep2 HeLa NRSF PCR1 2 NRSF HeLa-S3 ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001629 1629 GSM803478 Myers HudsonAlpha SL1322 PCR1x 2 exp wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep2 None Peaks Neuron-restrictive silencer transcription factor cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 NRSF PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep1 HeLa NRSF PCR1 1 NRSF HeLa-S3 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001629 1629 GSM803478 Myers HudsonAlpha SL679 PCR1x 1 exp MACS wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep1 None Peaks Neuron-restrictive silencer transcription factor cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 NRSF PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3GabpPcr1xPkRep2 HeLa GABP PCR1 2 GABP HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-18 2010-09-18 wgEncodeEH001504 1504 GSM803454 Myers HudsonAlpha SL611 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsHelas3GabpPcr1xPkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 GABP PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsHelas3GabpPcr1xPkRep1 HeLa GABP PCR1 1 GABP HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-18 2010-09-18 wgEncodeEH001504 1504 GSM803454 Myers HudsonAlpha SL610 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsHelas3GabpPcr1xPkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. cervical carcinoma Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment HeLa-S3 GABP PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsTaf1V0422111PkRep2 H1-neu TAF1 2 TAF1 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003266 3266 GSM1010805 Myers HudsonAlpha SL14594 v042211.1 2 exp MACS wgEncodeHaibTfbsH1neuronsTaf1V0422111PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-neurons TAF1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsTaf1V0422111PkRep1 H1-neu TAF1 1 TAF1 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003266 3266 GSM1010805 Myers HudsonAlpha SL13300 v042211.1 1 exp MACS wgEncodeHaibTfbsH1neuronsTaf1V0422111PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-neurons TAF1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsPol24h8V0422111PkRep2 H1-neu Pol2-4H8 2 Pol2-4H8 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003265 3265 GSM1010803 Myers HudsonAlpha SL14592 v042211.1 2 exp MACS wgEncodeHaibTfbsH1neuronsPol24h8V0422111PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-neurons Pol2-4H8 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsPol24h8V0422111PkRep1 H1-neu Pol2-4H8 1 Pol2-4H8 H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003265 3265 GSM1010803 Myers HudsonAlpha SL13298 v042211.1 1 exp MACS wgEncodeHaibTfbsH1neuronsPol24h8V0422111PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-neurons Pol2-4H8 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsNrsfV0422111PkRep2 H1-neu NRSF V11 2 NRSF H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003264 3264 GSM1010804 Myers HudsonAlpha SL14593 v042211.1 2 exp MACS wgEncodeHaibTfbsH1neuronsNrsfV0422111PkRep2 None Peaks Neuron-restrictive silencer transcription factor neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-neurons NRSF v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1neuronsNrsfV0422111PkRep1 H1-neu NRSF V11 1 NRSF H1-neurons ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003264 3264 GSM1010804 Myers HudsonAlpha SL13299 v042211.1 1 exp MACS wgEncodeHaibTfbsH1neuronsNrsfV0422111PkRep1 None Peaks Neuron-restrictive silencer transcription factor neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-neurons NRSF v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02PkRep2 A549 ZBTB33 ETH 2 ZBTB33 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002295 2295 GSM1010832 Myers HudsonAlpha SL6592 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02PkRep2 EtOH_0.02pct Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ZBTB33 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02PkRep1 A549 ZBTB33 ETH 1 ZBTB33 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002295 2295 GSM1010832 Myers HudsonAlpha SL6016 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Zbtb33V0422111Etoh02PkRep1 EtOH_0.02pct Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ZBTB33 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Yy1cV0422111Etoh02PkRep2 A549 YY1 EtOH 2 YY1_(SC-281) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002282 2282 GSM1010794 Myers HudsonAlpha SL5699 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Yy1cV0422111Etoh02PkRep2 EtOH_0.02pct Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 YY1 281 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Yy1cV0422111Etoh02PkRep1 A549 YY1 EtOH 1 YY1_(SC-281) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002282 2282 GSM1010794 Myers HudsonAlpha SL5357 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Yy1cV0422111Etoh02PkRep1 EtOH_0.02pct Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 YY1 281 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1V0422111Etoh02PkRep2 A549 USF Et V11 2 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002291 2291 GSM1010828 Myers HudsonAlpha SL7279 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Usf1V0422111Etoh02PkRep2 EtOH_0.02pct Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 USF-1 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1V0422111Etoh02PkRep1 A549 USF Et V11 1 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002291 2291 GSM1010828 Myers HudsonAlpha SL6593 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Usf1V0422111Etoh02PkRep1 EtOH_0.02pct Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 USF-1 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02PkRep2 A549 USF1 Et P1 2 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001539 1539 GSM803429 Myers HudsonAlpha SL1207 PCR1x 2 exp wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02PkRep2 EtOH_0.02pct Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 USF-1 EtOH PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02PkRep1 A549 USF1 Et P1 1 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001539 1539 GSM803429 Myers HudsonAlpha SL1080 PCR1x 1 exp wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02PkRep1 EtOH_0.02pct Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 USF-1 EtOH PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmPkRep2 A549 USF1 DEX 2 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001509 1509 GSM803457 Myers HudsonAlpha SL1206 PCR1x 2 exp wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmPkRep2 DEX_100nM Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 USF-1 DEX 100nM PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmPkRep1 A549 USF1 DEX 1 USF-1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001509 1509 GSM803457 Myers HudsonAlpha SL1079 PCR1x 1 exp wgEncodeHaibTfbsA549Usf1Pcr1xDex100nmPkRep1 DEX_100nM Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 USF-1 DEX 100nM PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tead4sc101184V0422111PkRep2 A549 TEAD4 V11 2 TEAD4_(SC-101184) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003273 3273 GSM1010868 Myers HudsonAlpha SL14702 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Tead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tead4sc101184V0422111PkRep1 A549 TEAD4 V11 1 TEAD4_(SC-101184) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-28 wgEncodeEH003273 3273 GSM1010868 Myers HudsonAlpha SL13479 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Tead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tcf12V0422111Etoh02PkRep2 A549 TCF12 EtOH 2 TCF12 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002312 2312 GSM1010746 Myers HudsonAlpha SL8076 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Tcf12V0422111Etoh02PkRep2 EtOH_0.02pct Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 TCF12 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Tcf12V0422111Etoh02PkRep1 A549 TCF12 EtOH 1 TCF12 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002312 2312 GSM1010746 Myers HudsonAlpha SL7114 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Tcf12V0422111Etoh02PkRep1 EtOH_0.02pct Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 TCF12 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Taf1V0422111Etoh02PkRep2 A549 TAF1 EtOH 2 TAF1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002275 2275 GSM1010812 Myers HudsonAlpha SL5700 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Taf1V0422111Etoh02PkRep2 EtOH_0.02pct Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 TAF1 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Taf1V0422111Etoh02PkRep1 A549 TAF1 EtOH 1 TAF1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002275 2275 GSM1010812 Myers HudsonAlpha SL5358 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Taf1V0422111Etoh02PkRep1 EtOH_0.02pct Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 TAF1 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sp1V0422111Etoh02PkRep2 A549 SP1 EtOH 2 SP1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002274 2274 GSM1010813 Myers HudsonAlpha SL5701 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Sp1V0422111Etoh02PkRep2 EtOH_0.02pct Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 SP1 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sp1V0422111Etoh02PkRep1 A549 SP1 EtOH 1 SP1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002274 2274 GSM1010813 Myers HudsonAlpha SL5360 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Sp1V0422111Etoh02PkRep1 EtOH_0.02pct Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 SP1 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Six5V0422111Etoh02PkRep2 A549 SIX5 EtOH 2 SIX5 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002341 2341 GSM1010879 Myers HudsonAlpha SL8400 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Six5V0422111Etoh02PkRep2 EtOH_0.02pct Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 SIX5 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Six5V0422111Etoh02PkRep1 A549 SIX5 EtOH 1 SIX5 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002341 2341 GSM1010879 Myers HudsonAlpha SL7277 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Six5V0422111Etoh02PkRep1 EtOH_0.02pct Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 SIX5 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02PkRep2 A549 Sin3A EtOH 2 Sin3Ak-20 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002342 2342 GSM1010882 Myers HudsonAlpha SL8401 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02PkRep2 EtOH_0.02pct Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 Sin3Ak-20 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02PkRep1 A549 Sin3A EtOH 1 Sin3Ak-20 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002342 2342 GSM1010882 Myers HudsonAlpha SL7275 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Sin3ak20V0422111Etoh02PkRep1 EtOH_0.02pct Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 Sin3Ak-20 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Rad21V0422111PkRep2 A549 RAD21 V11 2 Rad21 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003272 3272 GSM1010761 Myers HudsonAlpha SL16300 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Rad21V0422111PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 RAD21 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Rad21V0422111PkRep1 A549 RAD21 V11 1 Rad21 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003272 3272 GSM1010761 Myers HudsonAlpha SL12634 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Rad21V0422111PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 RAD21 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02PkRep2 A549 Pol2 EtOH 2 Pol2 A549 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-12-15 2011-03-22 wgEncodeEH001493 1493 GSM803360 Myers HudsonAlpha SL334 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02PkRep2 EtOH_0.02pct Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 Pol2 EtOH PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02PkRep1 A549 Pol2 EtOH 1 Pol2 A549 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-12-15 2011-03-22 wgEncodeEH001493 1493 GSM803360 Myers HudsonAlpha SL245 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02PkRep1 EtOH_0.02pct Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 Pol2 EtOH PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmPkRep2 A549 Pol2 DEX 2 Pol2 A549 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-12-17 2011-03-22 wgEncodeEH001494 1494 GSM803361 Myers HudsonAlpha SL306 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmPkRep2 DEX_100nM Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 Pol2 DEX 100nM PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmPkRep1 A549 Pol2 DEX 1 Pol2 A549 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-12-17 2011-03-22 wgEncodeEH001494 1494 GSM803361 Myers HudsonAlpha SL244 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsA549Pol2Pcr2xDex100nmPkRep1 DEX_100nM Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 Pol2 DEX 100nM PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pbx3V0422111PkRep2 A549 PBx3 V11 2 Pbx3 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003255 3255 GSM1010755 Myers HudsonAlpha SL16043 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Pbx3V0422111PkRep2 None Peaks Pbx 3 (D-17) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 PBx3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Pbx3V0422111PkRep1 A549 PBx3 V11 1 Pbx3 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003255 3255 GSM1010755 Myers HudsonAlpha SL13476 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Pbx3V0422111PkRep1 None Peaks Pbx 3 (D-17) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 PBx3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549P300V0422111Etoh02PkRep2 A549 p300 EtOH 2 p300 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002292 2292 GSM1010827 Myers HudsonAlpha SL7115 v042211.1 2 exp MACS wgEncodeHaibTfbsA549P300V0422111Etoh02PkRep2 EtOH_0.02pct Peaks EP300(c-20) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 p300 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549P300V0422111Etoh02PkRep1 A549 p300 EtOH 1 p300 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-29 2012-05-29 wgEncodeEH002292 2292 GSM1010827 Myers HudsonAlpha SL6437 v042211.1 1 exp MACS wgEncodeHaibTfbsA549P300V0422111Etoh02PkRep1 EtOH_0.02pct Peaks EP300(c-20) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 p300 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549NrsfV0422111Etoh02PkRep2 A549 NRSF EtOH 2 NRSF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002311 2311 GSM1010749 Myers HudsonAlpha SL8075 v042211.1 2 exp MACS wgEncodeHaibTfbsA549NrsfV0422111Etoh02PkRep2 EtOH_0.02pct Peaks Neuron-restrictive silencer transcription factor epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 NRSF EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549NrsfV0422111Etoh02PkRep1 A549 NRSF EtOH 1 NRSF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002311 2311 GSM1010749 Myers HudsonAlpha SL7110 v042211.1 1 exp MACS wgEncodeHaibTfbsA549NrsfV0422111Etoh02PkRep1 EtOH_0.02pct Peaks Neuron-restrictive silencer transcription factor epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 NRSF EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549MaxV0422111PkRep2 A549 Max V11 2 Max A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003251 3251 GSM1010728 Myers HudsonAlpha SL13754 v042211.1 2 exp MACS wgEncodeHaibTfbsA549MaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549MaxV0422111PkRep1 A549 Max V11 1 Max A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003251 3251 GSM1010728 Myers HudsonAlpha SL12638 v042211.1 1 exp MACS wgEncodeHaibTfbsA549MaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549JundV0416102Etoh02PkRep2 A549 JunD EtOH 2 JunD A549 ChipSeq ENCODE Jul 2012 Freeze 2012-08-29 2013-05-29 wgEncodeEH002327 2327 GSM1010723 Myers HudsonAlpha SL4698 v041610.2 2 exp MACS wgEncodeHaibTfbsA549JundV0416102Etoh02PkRep2 EtOH_0.02pct Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 JunD EtOH 0.02pct v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549JundV0416102Etoh02PkRep1 A549 JunD EtOH 1 JunD A549 ChipSeq ENCODE Jul 2012 Freeze 2012-08-29 2013-05-29 wgEncodeEH002327 2327 GSM1010723 Myers HudsonAlpha SL3900 v041610.2 1 exp MACS wgEncodeHaibTfbsA549JundV0416102Etoh02PkRep1 EtOH_0.02pct Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 JunD EtOH 0.02pct v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex5nmPkRep2 A549 GR DX5nM 2 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-09 2011-03-16 wgEncodeEH001492 1492 GSM803359 Myers HudsonAlpha SL881 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsA549GrPcr1xDex5nmPkRep2 DEX_5nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 5 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 5nM PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex5nmPkRep1 A549 GR DX5nM 1 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-09 2010-09-09 wgEncodeEH001492 1492 GSM803359 Myers HudsonAlpha SL880 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsA549GrPcr1xDex5nmPkRep1 DEX_5nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 5 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 5nM PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex50nmPkRep2 A549 GR DX50nM 2 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-09 2010-09-09 wgEncodeEH001491 1491 GSM803358 Myers HudsonAlpha SL883 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsA549GrPcr1xDex50nmPkRep2 DEX_50nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 50 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 50nM PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex50nmPkRep1 A549 GR DX50nM 1 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-09 2010-09-09 wgEncodeEH001491 1491 GSM803358 Myers HudsonAlpha SL882 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsA549GrPcr1xDex50nmPkRep1 DEX_50nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 50 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 50nM PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex500pmPkRep2 A549 GR DX.5nM 2 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-09 2010-09-09 wgEncodeEH001490 1490 GSM803357 Myers HudsonAlpha SL885 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsA549GrPcr1xDex500pmPkRep2 DEX_500pM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 500 pM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 500pM PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr1xDex500pmPkRep1 A549 GR DX.5nM 1 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-09 2010-09-09 wgEncodeEH001490 1490 GSM803357 Myers HudsonAlpha SL884 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsA549GrPcr1xDex500pmPkRep1 DEX_500pM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 500 pM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 500pM PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr2xDex100nmPkRep2 A549 GR DX100nM 2 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2011-03-22 wgEncodeEH001555 1555 GSM803371 Myers HudsonAlpha SL304 hg19 PCR2x 2 exp MACS wgEncodeHaibTfbsA549GrPcr2xDex100nmPkRep2 DEX_100nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 100nM PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GrPcr2xDex100nmPkRep1 A549 GR DX100nM 1 GR A549 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2011-03-22 wgEncodeEH001555 1555 GSM803371 Myers HudsonAlpha SL246 hg19 PCR2x 1 exp MACS wgEncodeHaibTfbsA549GrPcr2xDex100nmPkRep1 DEX_100nM Peaks Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 GR DEX 100nM PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Gata3V0422111PkRep2 A549 GATA3 V11 2 GATA3_(SC-268) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003250 3250 GSM1010727 Myers HudsonAlpha SL13283 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Gata3V0422111PkRep2 None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 GATA3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Gata3V0422111PkRep1 A549 GATA3 V11 1 GATA3_(SC-268) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-24 2013-04-24 wgEncodeEH003250 3250 GSM1010727 Myers HudsonAlpha SL12399 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Gata3V0422111PkRep1 None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 GATA3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GabpV0422111Etoh02PkRep2 A549 GABP EtOH 2 GABP A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002294 2294 GSM1010833 Myers HudsonAlpha SL6595 v042211.1 2 exp MACS wgEncodeHaibTfbsA549GabpV0422111Etoh02PkRep2 EtOH_0.02pct Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 GABP EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549GabpV0422111Etoh02PkRep1 A549 GABP EtOH 1 GABP A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002294 2294 GSM1010833 Myers HudsonAlpha SL6015 v042211.1 1 exp MACS wgEncodeHaibTfbsA549GabpV0422111Etoh02PkRep1 EtOH_0.02pct Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 GABP EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa2V0416102Etoh02PkRep2 A549 FOXA2 EtOH 2 FOXA2_(SC-6554) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-08-29 2013-05-29 wgEncodeEH002326 2326 GSM1010724 Myers HudsonAlpha SL3253 v041610.2 2 exp MACS wgEncodeHaibTfbsA549Foxa2V0416102Etoh02PkRep2 EtOH_0.02pct Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 FOXA2 EtOH v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa2V0416102Etoh02PkRep1 A549 FOXA2 EtOH 1 FOXA2_(SC-6554) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-08-29 2013-05-29 wgEncodeEH002326 2326 GSM1010724 Myers HudsonAlpha SL3077 v041610.2 1 exp MACS wgEncodeHaibTfbsA549Foxa2V0416102Etoh02PkRep1 EtOH_0.02pct Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 FOXA2 EtOH v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmPkRep2 A549 FOXA1 DEX 2 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002293 2293 GSM1010826 Myers HudsonAlpha SL3250 v041610.2 2 exp MACS wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmPkRep2 DEX_100nM Peaks This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 FOXA1 101058 DEX 100nM v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmPkRep1 A549 FOXA1 DEX 1 FOXA1_(SC-101058) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2012-05-30 wgEncodeEH002293 2293 GSM1010826 Myers HudsonAlpha SL2666 v041610.2 1 exp MACS wgEncodeHaibTfbsA549Foxa1V0416102Dex100nmPkRep1 DEX_100nM Peaks This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 FOXA1 101058 DEX 100nM v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Fosl2V0422111Etoh02PkRep2 A549 FOSL2 EtOH 2 FOSL2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002310 2310 GSM1010748 Myers HudsonAlpha SL8077 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Fosl2V0422111Etoh02PkRep2 EtOH_0.02pct Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 FOSL2 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Fosl2V0422111Etoh02PkRep1 A549 FOSL2 EtOH 1 FOSL2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002310 2310 GSM1010748 Myers HudsonAlpha SL7116 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Fosl2V0422111Etoh02PkRep1 EtOH_0.02pct Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 FOSL2 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ets1V0422111Etoh02PkRep2 A549 ETS1 EtOH 2 ETS1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002290 2290 GSM1010829 Myers HudsonAlpha SL7108 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Ets1V0422111Etoh02PkRep2 EtOH_0.02pct Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ETS1 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ets1V0422111Etoh02PkRep1 A549 ETS1 EtOH 1 ETS1 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002290 2290 GSM1010829 Myers HudsonAlpha SL6600 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Ets1V0422111Etoh02PkRep1 EtOH_0.02pct Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ETS1 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Elf1V0422111Etoh02PkRep2 A549 ELF1 EtOH 2 ELF1_(SC-631) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002289 2289 GSM1010790 Myers HudsonAlpha SL7113 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Elf1V0422111Etoh02PkRep2 EtOH_0.02pct Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ELF1 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Elf1V0422111Etoh02PkRep1 A549 ELF1 EtOH 1 ELF1_(SC-631) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002289 2289 GSM1010790 Myers HudsonAlpha SL6436 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Elf1V0422111Etoh02PkRep1 EtOH_0.02pct Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ELF1 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549E2f6V0422111PkRep2 A549 E2F6 V11 2 E2F6 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003244 3244 GSM1010766 Myers HudsonAlpha SL14581 v042211.1 2 exp MACS wgEncodeHaibTfbsA549E2f6V0422111PkRep2 None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 E2F6 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549E2f6V0422111PkRep1 A549 E2F6 V11 1 E2F6 A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEH003244 3244 GSM1010766 Myers HudsonAlpha SL13319 v042211.1 1 exp MACS wgEncodeHaibTfbsA549E2f6V0422111PkRep1 None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 E2F6 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02PkRep2 A549 CTCF EtOH 2 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001508 1508 GSM803456 Myers HudsonAlpha SL1078 PCR1x 2 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02PkRep2 EtOH_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 CTCF 5916 EtOH PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02PkRep1 A549 CTCF EtOH 1 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001508 1508 GSM803456 Myers HudsonAlpha SL1205 PCR1x 1 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xEtoh02PkRep1 EtOH_0.02pct Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 CTCF 5916 EtOH PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmPkRep2 A549 CTCF DEX 2 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001507 1507 GSM803453 Myers HudsonAlpha SL1077 PCR1x 2 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmPkRep2 DEX_100nM Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 CTCF 5916 DEX 100nM PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmPkRep1 A549 CTCF DEX 1 CTCF_(SC-5916) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001507 1507 GSM803453 Myers HudsonAlpha SL1204 PCR1x 1 exp wgEncodeHaibTfbsA549Ctcfsc5916Pcr1xDex100nmPkRep1 DEX_100nM Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 CTCF 5916 DEX 100nM PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmPkRep2 A549 CREB1 DEX 2 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002323 2323 GSM1010719 Myers HudsonAlpha SL3897 v041610.2 2 exp MACS wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmPkRep2 DEX_100nM Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 CREB1 DEX 100nM v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmPkRep1 A549 CREB1 DEX 1 CREB1_(SC-240) A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002323 2323 GSM1010719 Myers HudsonAlpha SL1667 v041610.2 1 exp MACS wgEncodeHaibTfbsA549Creb1sc240V0416102Dex100nmPkRep1 DEX_100nM Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) 1 h with 100 nM Dexamethasone (Myers) Regions of enriched signal in experiment A549 CREB1 DEX 100nM v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Cebpbsc150V0422111PkRep2 A549 CEBPB V11 2 CEBPB_(SC-150) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003271 3271 GSM1010871 Myers HudsonAlpha SL16299 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Cebpbsc150V0422111PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 CEBPB v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Cebpbsc150V0422111PkRep1 A549 CEBPB V11 1 CEBPB_(SC-150) A549 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003271 3271 GSM1010871 Myers HudsonAlpha SL12637 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Cebpbsc150V0422111PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment A549 CEBPB v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Bcl3V0422111Etoh02PkRep2 A549 BCL3 EtOH 2 BCL3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002303 2303 GSM1010775 Myers HudsonAlpha SL7109 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Bcl3V0422111Etoh02PkRep2 EtOH_0.02pct Peaks This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 BCL3 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Bcl3V0422111Etoh02PkRep1 A549 BCL3 EtOH 1 BCL3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-12 2012-06-12 wgEncodeEH002303 2303 GSM1010775 Myers HudsonAlpha SL6596 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Bcl3V0422111Etoh02PkRep1 EtOH_0.02pct Peaks This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 BCL3 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Atf3V0422111Etoh02PkRep2 A549 ATF3 EtOH 2 ATF3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002288 2288 GSM1010789 Myers HudsonAlpha SL7273 v042211.1 2 exp MACS wgEncodeHaibTfbsA549Atf3V0422111Etoh02PkRep2 EtOH_0.02pct Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ATF3 EtOH v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsA549Atf3V0422111Etoh02PkRep1 A549 ATF3 EtOH 1 ATF3 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-08-16 2012-05-16 wgEncodeEH002288 2288 GSM1010789 Myers HudsonAlpha SL6010 v042211.1 1 exp MACS wgEncodeHaibTfbsA549Atf3V0422111Etoh02PkRep1 EtOH_0.02pct Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) 1 h with 0.02% Ethanol (Myers) Regions of enriched signal in experiment A549 ATF3 EtOH v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb7asc34508V0416101PkRep2 K562 ZBTB7A 2 ZBTB7A_(SC-34508) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001620 1620 GSM803473 Myers HudsonAlpha SL3183 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Zbtb7asc34508V0416101PkRep2 None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ZBTB7A v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb7asc34508V0416101PkRep1 K562 ZBTB7A 1 ZBTB7A_(SC-34508) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001620 1620 GSM803473 Myers HudsonAlpha SL2265 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Zbtb7asc34508V0416101PkRep1 None Peaks Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals (By similarity). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ZBTB7A v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb33Pcr1xPkRep2 K562 ZBTB33 2 ZBTB33 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-16 2011-06-16 wgEncodeEH001569 1569 GSM803504 Myers HudsonAlpha SL1320 PCR1x 2 exp MACS wgEncodeHaibTfbsK562Zbtb33Pcr1xPkRep2 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ZBTB33 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Zbtb33Pcr1xPkRep1 K562 ZBTB33 1 ZBTB33 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-16 2011-06-16 wgEncodeEH001569 1569 GSM803504 Myers HudsonAlpha SL1114 PCR1x 1 exp MACS wgEncodeHaibTfbsK562Zbtb33Pcr1xPkRep1 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ZBTB33 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1sc281V0416101PkRep2 K562 YY1 V101 2 YY1_(SC-281) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEH001584 1584 GSM803446 Myers HudsonAlpha SL2944 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Yy1sc281V0416101PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 YY1 281 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1sc281V0416101PkRep1 K562 YY1 V101 1 YY1_(SC-281) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEH001584 1584 GSM803446 Myers HudsonAlpha SL2203 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Yy1sc281V0416101PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 YY1 281 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1V0416102PkRep2 K562 YY1 V102 2 YY1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001623 1623 GSM803470 Myers HudsonAlpha SL3071 v041610.2 2 exp MACS wgEncodeHaibTfbsK562Yy1V0416102PkRep2 None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 YY1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Yy1V0416102PkRep1 K562 YY1 V102 1 YY1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001623 1623 GSM803470 Myers HudsonAlpha SL2946 v041610.2 1 exp MACS wgEncodeHaibTfbsK562Yy1V0416102PkRep1 None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 YY1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Usf1V0416101PkRep2 K562 USF1 V101 2 USF-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001583 1583 GSM803441 Myers HudsonAlpha SL3166 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Usf1V0416101PkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 USF-1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Usf1V0416101PkRep1 K562 USF1 V101 1 USF-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001583 1583 GSM803441 Myers HudsonAlpha SL3163 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Usf1V0416101PkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 USF-1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Trim28sc81411V0422111PkRep2 K562 TRIM28 V11 2 TRIM28_(SC-81411) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH003210 3210 GSM1010849 Myers HudsonAlpha SL9830 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Trim28sc81411V0422111PkRep2 None Peaks The protein encoded by this gene mediates transcriptional control by interaction with the Kruppel-associated box repression domain found in many transcription factors. The protein localizes to the nucleus and is thought to associate with specific chromatin regions. The protein is a member of the tripartite motif family. This tripartite motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 TRIM28 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Trim28sc81411V0422111PkRep1 K562 TRIM28 V11 1 TRIM28_(SC-81411) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH003210 3210 GSM1010849 Myers HudsonAlpha SL8672 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Trim28sc81411V0422111PkRep1 None Peaks The protein encoded by this gene mediates transcriptional control by interaction with the Kruppel-associated box repression domain found in many transcription factors. The protein localizes to the nucleus and is thought to associate with specific chromatin regions. The protein is a member of the tripartite motif family. This tripartite motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 TRIM28 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Thap1sc98174V0416101PkRep2 K562 THAP1 V101 2 THAP1_(SC-98174) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001655 1655 GSM803408 Myers HudsonAlpha SL3186 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Thap1sc98174V0416101PkRep2 None Peaks The protein encoded by this gene contains a THAP domain, a conserved DNA-binding domain. This protein colocalizes with the apoptosis response protein PAWR/PAR-4 in promyelocytic leukemia (PML) nuclear bodies, and functions as a proapoptotic factor that links PAWR to PML nuclear bodies. Alternatively spliced transcript variants encoding distinct isoforms have been observed. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 THAP1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Thap1sc98174V0416101PkRep1 K562 THAP1 V101 1 THAP1_(SC-98174) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001655 1655 GSM803408 Myers HudsonAlpha SL2202 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Thap1sc98174V0416101PkRep1 None Peaks The protein encoded by this gene contains a THAP domain, a conserved DNA-binding domain. This protein colocalizes with the apoptosis response protein PAWR/PAR-4 in promyelocytic leukemia (PML) nuclear bodies, and functions as a proapoptotic factor that links PAWR to PML nuclear bodies. Alternatively spliced transcript variants encoding distinct isoforms have been observed. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 THAP1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Tead4sc101184V0422111PkRep2 K562 TEAD4 V11 2 TEAD4_(SC-101184) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002333 2333 GSM1010895 Myers HudsonAlpha SL7841 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Tead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Tead4sc101184V0422111PkRep1 K562 TEAD4 V11 1 TEAD4_(SC-101184) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002333 2333 GSM1010895 Myers HudsonAlpha SL7571 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Tead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf7sc101167V0416101PkRep2 K562 TAF7 V101 2 TAF7_(SC-101167) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001654 1654 GSM803407 Myers HudsonAlpha SL3568 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Taf7sc101167V0416101PkRep2 None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 TAF7 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf7sc101167V0416101PkRep1 K562 TAF7 V101 1 TAF7_(SC-101167) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001654 1654 GSM803407 Myers HudsonAlpha SL3274 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Taf7sc101167V0416101PkRep1 None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 TAF7 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf1V0416101PkRep2 K562 TAF1 V101 2 TAF1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001582 1582 GSM803431 Myers HudsonAlpha SL2942 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Taf1V0416101PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 TAF1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Taf1V0416101PkRep1 K562 TAF1 V101 1 TAF1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001582 1582 GSM803431 Myers HudsonAlpha SL2941 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Taf1V0416101PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 TAF1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Stat5asc74442V0422111PkRep2 K562 STAT5A V11 2 STAT5A_(SC-74442) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002347 2347 GSM1010877 Myers HudsonAlpha SL9116 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Stat5asc74442V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 STAT5A v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Stat5asc74442V0422111PkRep1 K562 STAT5A V11 1 STAT5A_(SC-74442) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002347 2347 GSM1010877 Myers HudsonAlpha SL8673 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Stat5asc74442V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 STAT5A v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562SrfV0416101PkRep2 K562 SRF V101 2 SRF K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001600 1600 GSM803520 Myers HudsonAlpha SL3272 v041610.1 2 exp MACS wgEncodeHaibTfbsK562SrfV0416101PkRep2 None Peaks Serum response transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SRF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562SrfV0416101PkRep1 K562 SRF V101 1 SRF K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001600 1600 GSM803520 Myers HudsonAlpha SL3162 v041610.1 1 exp MACS wgEncodeHaibTfbsK562SrfV0416101PkRep1 None Peaks Serum response transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SRF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp2sc643V0416102PkRep2 K562 SP2 V102 2 SP2_(SC-643) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001653 1653 GSM803402 Myers HudsonAlpha SL3361 v041610.2 2 exp MACS wgEncodeHaibTfbsK562Sp2sc643V0416102PkRep2 None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SP2 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp2sc643V0416102PkRep1 K562 SP2 V102 1 SP2_(SC-643) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001653 1653 GSM803402 Myers HudsonAlpha SL2951 v041610.2 1 exp MACS wgEncodeHaibTfbsK562Sp2sc643V0416102PkRep1 None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SP2 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp1Pcr1xPkRep2 K562 SP1 PCR1 2 SP1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH001578 1578 GSM803505 Myers HudsonAlpha SL1510 PCR1x 2 exp MACS wgEncodeHaibTfbsK562Sp1Pcr1xPkRep2 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SP1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sp1Pcr1xPkRep1 K562 SP1 PCR1 1 SP1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-30 2011-06-30 wgEncodeEH001578 1578 GSM803505 Myers HudsonAlpha SL1197 PCR1x 1 exp MACS wgEncodeHaibTfbsK562Sp1Pcr1xPkRep1 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SP1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5V0416101PkRep2 K562 SIX5 V101 2 SIX5 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001664 1664 GSM803378 Myers HudsonAlpha SL3990 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Six5V0416101PkRep2 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SIX5 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5V0416101PkRep1 K562 SIX5 V101 1 SIX5 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001664 1664 GSM803378 Myers HudsonAlpha SL3924 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Six5V0416101PkRep1 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SIX5 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5Pcr1xPkRep2 K562 SIX5 PCR1 2 SIX5 K562 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001483 1483 GSM803383 Myers HudsonAlpha SL986 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsK562Six5Pcr1xPkRep2 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SIX5 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Six5Pcr1xPkRep1 K562 SIX5 PCR1 1 SIX5 K562 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-26 2010-07-26 wgEncodeEH001483 1483 GSM803383 Myers HudsonAlpha SL842 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsK562Six5Pcr1xPkRep1 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 SIX5 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sin3ak20V0416101PkRep2 K562 Sin3A V101 2 Sin3Ak-20 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-03 2011-09-03 wgEncodeEH001607 1607 GSM803525 Myers HudsonAlpha SL3496 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Sin3ak20V0416101PkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Sin3ak20V0416101PkRep1 K562 Sin3A V101 1 Sin3Ak-20 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-03 2011-09-03 wgEncodeEH001607 1607 GSM803525 Myers HudsonAlpha SL3273 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Sin3ak20V0416101PkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Sin3Ak-20 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Rad21V0416102PkRep2 K562 RAD21 V102 2 Rad21 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH001585 1585 GSM803447 Myers HudsonAlpha SL3072 v041610.2 2 exp MACS wgEncodeHaibTfbsK562Rad21V0416102PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 RAD21 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Rad21V0416102PkRep1 K562 RAD21 V102 1 Rad21 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH001585 1585 GSM803447 Myers HudsonAlpha SL2947 v041610.2 1 exp MACS wgEncodeHaibTfbsK562Rad21V0416102PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 RAD21 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pu1Pcr1xPkRep2 K562 PU.1 PCR1 2 PU.1 K562 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001482 1482 GSM803384 Myers HudsonAlpha SL705 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsK562Pu1Pcr1xPkRep2 None Peaks PU.1 (H-135) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 PU.1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pu1Pcr1xPkRep1 K562 PU.1 PCR1 1 PU.1 K562 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001482 1482 GSM803384 Myers HudsonAlpha SL646 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsK562Pu1Pcr1xPkRep1 None Peaks PU.1 (H-135) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 PU.1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol24h8V0416101PkRep2 K562 Pol2-4H8 V101 2 Pol2-4H8 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001581 1581 GSM803443 Myers HudsonAlpha SL2940 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Pol24h8V0416101PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol24h8V0416101PkRep1 K562 Pol2-4H8 V101 1 Pol2-4H8 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001581 1581 GSM803443 Myers HudsonAlpha SL2939 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Pol24h8V0416101PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Pol2-4H8 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol2V0416101PkRep2 K562 Pol2 V101 2 Pol2 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001633 1633 GSM803410 Myers HudsonAlpha SL3820 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Pol2V0416101PkRep2 None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Pol2 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pol2V0416101PkRep1 K562 Pol2 V101 1 Pol2 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001633 1633 GSM803410 Myers HudsonAlpha SL3819 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Pol2V0416101PkRep1 None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Pol2 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pmlsc71910V0422111PkRep2 K562 PML V11 2 PML_(SC-71910) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002320 2320 GSM1010722 Myers HudsonAlpha SL8137 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Pmlsc71910V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 PML v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Pmlsc71910V0422111PkRep1 K562 PML V11 1 PML_(SC-71910) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002320 2320 GSM1010722 Myers HudsonAlpha SL7894 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Pmlsc71910V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 PML v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562NrsfV0416102PkRep2 K562 NRSF V102 2 NRSF K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001638 1638 GSM803440 Myers HudsonAlpha SL3822 v041610.2 2 exp MACS wgEncodeHaibTfbsK562NrsfV0416102PkRep2 None Peaks Neuron-restrictive silencer transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 NRSF v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562NrsfV0416102PkRep1 K562 NRSF V102 1 NRSF K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001638 1638 GSM803440 Myers HudsonAlpha SL3821 v041610.2 1 exp MACS wgEncodeHaibTfbsK562NrsfV0416102PkRep1 None Peaks Neuron-restrictive silencer transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 NRSF v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Nr2f2sc271940V0422111PkRep2 K562 NR2F2 V11 2 NR2F2_(SC-271940) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002382 2382 GSM1010782 Myers HudsonAlpha SL8577 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Nr2f2sc271940V0422111PkRep2 None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 NR2F2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Nr2f2sc271940V0422111PkRep1 K562 NR2F2 V11 1 NR2F2_(SC-271940) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002382 2382 GSM1010782 Myers HudsonAlpha SL8143 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Nr2f2sc271940V0422111PkRep1 None Peaks This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 NR2F2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Mef2aV0416101PkRep2 K562 MEF2A V101 2 MEF2A K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001663 1663 GSM803379 Myers HudsonAlpha SL3925 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Mef2aV0416101PkRep2 None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 MEF2A v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Mef2aV0416101PkRep1 K562 MEF2A V101 1 MEF2A K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001663 1663 GSM803379 Myers HudsonAlpha SL1794 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Mef2aV0416101PkRep1 None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 MEF2A v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562MaxV0416102PkRep2 K562 Max V102 2 Max K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001605 1605 GSM803523 Myers HudsonAlpha SL3070 v041610.2 2 exp wgEncodeHaibTfbsK562MaxV0416102PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Max v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562MaxV0416102PkRep1 K562 Max V102 1 Max K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001605 1605 GSM803523 Myers HudsonAlpha SL2945 v041610.2 1 exp wgEncodeHaibTfbsK562MaxV0416102PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Max v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Hdac2sc6296V0416102PkRep2 K562 HDAC2 V102 2 HDAC2_(SC-6296) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001622 1622 GSM803471 Myers HudsonAlpha SL3359 v041610.2 2 exp MACS wgEncodeHaibTfbsK562Hdac2sc6296V0416102PkRep2 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 HDAC2 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Hdac2sc6296V0416102PkRep1 K562 HDAC2 V102 1 HDAC2_(SC-6296) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-23 2011-09-23 wgEncodeEH001622 1622 GSM803471 Myers HudsonAlpha SL2952 v041610.2 1 exp MACS wgEncodeHaibTfbsK562Hdac2sc6296V0416102PkRep1 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 HDAC2 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Gata2sc267Pcr1xPkRep2 K562 GATA2 PCR1 2 GATA2_(SC-267) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-28 2011-06-28 wgEncodeEH001576 1576 GSM803540 Myers HudsonAlpha SL1665 PCR1x 2 exp MACS wgEncodeHaibTfbsK562Gata2sc267Pcr1xPkRep2 None Peaks This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded program plays an essential role in regulation transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 GATA2 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Gata2sc267Pcr1xPkRep1 K562 GATA2 PCR1 1 GATA2_(SC-267) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-28 2011-06-28 wgEncodeEH001576 1576 GSM803540 Myers HudsonAlpha SL1430 PCR1x 1 exp MACS wgEncodeHaibTfbsK562Gata2sc267Pcr1xPkRep1 None Peaks This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded program plays an essential role in regulation transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 GATA2 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562GabpV0416101PkRep2 K562 GABP V101 2 GABP K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001604 1604 GSM803524 Myers HudsonAlpha SL3356 v041610.1 2 exp wgEncodeHaibTfbsK562GabpV0416101PkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 GABP v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562GabpV0416101PkRep1 K562 GABP V101 1 GABP K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-04 2010-12-01 2011-09-01 wgEncodeEH001604 1604 GSM803524 Myers HudsonAlpha SL2943 v041610.1 1 exp wgEncodeHaibTfbsK562GabpV0416101PkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 GABP v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep2 K562 FOSL1 V101 2 FOSL1_(SC-183) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001637 1637 GSM803439 Myers HudsonAlpha SL3187 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep2 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 FOSL1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep1 K562 FOSL1 V101 1 FOSL1_(SC-183) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001637 1637 GSM803439 Myers HudsonAlpha SL2349 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep1 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 FOSL1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ets1V0416101PkRep2 K562 ETS1 V101 2 ETS1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001580 1580 GSM803442 Myers HudsonAlpha SL3182 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Ets1V0416101PkRep2 None Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ETS1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ets1V0416101PkRep1 K562 ETS1 V101 1 ETS1 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-10-25 2011-07-25 wgEncodeEH001580 1580 GSM803442 Myers HudsonAlpha SL2262 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Ets1V0416101PkRep1 None Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ETS1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Elf1sc631V0416102PkRep2 K562 ELF1 V102 2 ELF1_(SC-631) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001619 1619 GSM803494 Myers HudsonAlpha SL3360 v041610.2 2 exp MACS wgEncodeHaibTfbsK562Elf1sc631V0416102PkRep2 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ELF1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Elf1sc631V0416102PkRep1 K562 ELF1 V102 1 ELF1_(SC-631) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001619 1619 GSM803494 Myers HudsonAlpha SL2950 v041610.2 1 exp MACS wgEncodeHaibTfbsK562Elf1sc631V0416102PkRep1 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ELF1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Egr1V0416101PkRep2 K562 Egr-1 V101 2 Egr-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001646 1646 GSM803414 Myers HudsonAlpha SL3497 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Egr1V0416101PkRep2 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Egr-1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Egr1V0416101PkRep1 K562 Egr-1 V101 1 Egr-1 K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001646 1646 GSM803414 Myers HudsonAlpha SL3164 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Egr1V0416101PkRep1 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 Egr-1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562E2f6V0416102PkRep2 K562 E2F6 V102 2 E2F6 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001598 1598 GSM803469 Myers HudsonAlpha SL3073 v041610.2 2 exp MACS wgEncodeHaibTfbsK562E2f6V0416102PkRep2 None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 E2F6 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562E2f6V0416102PkRep1 K562 E2F6 V102 1 E2F6 K562 ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001598 1598 GSM803469 Myers HudsonAlpha SL2948 v041610.2 1 exp MACS wgEncodeHaibTfbsK562E2f6V0416102PkRep1 None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 E2F6 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562CtcfcPcr1xPkRep2 K562 CTCF PCR1 2 CTCF_(SC-5916) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002279 2279 GSM1010820 Myers HudsonAlpha SL5605 PCR1x 2 exp MACS wgEncodeHaibTfbsK562CtcfcPcr1xPkRep2 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 CTCF 5916 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562CtcfcPcr1xPkRep1V2 K562 CTCF PCR1 1 CTCF_(SC-5916) K562 ChipSeq ENCODE Mar 2012 Freeze 2012-03-21 2012-12-21 wgEncodeEH002279 2279 GSM1010820 Myers HudsonAlpha SL3075 PCR1x 1 exp MACS wgEncodeHaibTfbsK562CtcfcPcr1xPkRep1V2 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 CTCF 5916 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ctcflsc98982V0416101PkRep2 K562 CTCFL V101 2 CTCFL_(SC-98982) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001652 1652 GSM803401 Myers HudsonAlpha SL3972 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Ctcflsc98982V0416101PkRep2 None Peaks CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily in the nucleus of somatic cells. CTCF and the protein encoded by this gene are normally expressed in a mutually exclusive pattern that correlates with resetting of methylation marks during male germ cell differentiation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 CTCFL v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Ctcflsc98982V0416101PkRep1 K562 CTCFL V101 1 CTCFL_(SC-98982) K562 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001652 1652 GSM803401 Myers HudsonAlpha SL3189 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Ctcflsc98982V0416101PkRep1 None Peaks CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily in the nucleus of somatic cells. CTCF and the protein encoded by this gene are normally expressed in a mutually exclusive pattern that correlates with resetting of methylation marks during male germ cell differentiation. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 CTCFL v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Creb1sc240V0422111PkRep2 K562 CREB1 V11 2 CREB1_(SC-240) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003230 3230 GSM1010890 Myers HudsonAlpha SL13293 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Creb1sc240V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CREB1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Creb1sc240V0422111PkRep1 K562 CREB1 V11 1 CREB1_(SC-240) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003230 3230 GSM1010890 Myers HudsonAlpha SL12420 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Creb1sc240V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CREB1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cebpdsc636V0422111PkRep2 K562 CEBPD V11 2 CEBPD_(SC-636) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEH003432 3432 GSM1010906 Myers HudsonAlpha SL13317 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Cebpdsc636V0422111PkRep2 None Peaks The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CEBPD v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIBd Regulation 
wgEncodeHaibTfbsK562Cebpdsc636V0422111PkRep1 K562 CEBPD V11 1 CEBPD_(SC-636) K562 ChipSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEH003432 3432 GSM1010906 Myers HudsonAlpha SL11280 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Cebpdsc636V0422111PkRep1 None Peaks The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CEBPD v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIBd Regulation 
wgEncodeHaibTfbsK562Cebpbsc150V0422111PkRep2 K562 CEBPB V11 2 CEBPB_(SC-150) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002346 2346 GSM1010878 Myers HudsonAlpha SL9547 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Cebpbsc150V0422111PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CEBPB v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cebpbsc150V0422111PkRep1 K562 CEBPB V11 1 CEBPB_(SC-150) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002346 2346 GSM1010878 Myers HudsonAlpha SL8085 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Cebpbsc150V0422111PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CEBPB v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cbx3sc101004V0422111PkRep2 K562 CBX3 V11 2 CBX3_(SC-101004) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002383 2383 GSM1010732 Myers HudsonAlpha SL7568 v042211.1 2 exp MACS wgEncodeHaibTfbsK562Cbx3sc101004V0422111PkRep2 None Peaks At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CBX3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Cbx3sc101004V0422111PkRep1 K562 CBX3 V11 1 CBX3_(SC-101004) K562 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002383 2383 GSM1010732 Myers HudsonAlpha SL7105 v042211.1 1 exp MACS wgEncodeHaibTfbsK562Cbx3sc101004V0422111PkRep1 None Peaks At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment K562 CBX3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Bclaf101388Pcr1xPkRep2 K562 BCLAF1 2 BCLAF1_(SC-101388) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001571 1571 GSM803515 Myers HudsonAlpha SL1512 PCR1x 2 exp MACS wgEncodeHaibTfbsK562Bclaf101388Pcr1xPkRep2 None Peaks This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 BCLAF1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Bclaf101388Pcr1xPkRep1 K562 BCLAF1 1 BCLAF1_(SC-101388) K562 ChipSeq ENCODE Jan 2011 Freeze 2010-09-21 2011-06-21 wgEncodeEH001571 1571 GSM803515 Myers HudsonAlpha SL1273 PCR1x 1 exp MACS wgEncodeHaibTfbsK562Bclaf101388Pcr1xPkRep1 None Peaks This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 BCLAF1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Atf3V0416101PkRep2 K562 ATF3 V101 2 ATF3 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001662 1662 GSM803380 Myers HudsonAlpha SL3926 v041610.1 2 exp MACS wgEncodeHaibTfbsK562Atf3V0416101PkRep2 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ATF3 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsK562Atf3V0416101PkRep1 K562 ATF3 V101 1 ATF3 K562 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001662 1662 GSM803380 Myers HudsonAlpha SL3184 v041610.1 1 exp MACS wgEncodeHaibTfbsK562Atf3V0416101PkRep1 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment K562 ATF3 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescYy1sc281V0416102PkRep2 hESC YY1 V102 2 YY1_(SC-281) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001567 1567 GSM803513 Myers HudsonAlpha SL1967 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescYy1sc281V0416102PkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC YY1 281 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescYy1sc281V0416102PkRep1 hESC YY1 V102 1 YY1_(SC-281) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001567 1567 GSM803513 Myers HudsonAlpha SL1657 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescYy1sc281V0416102PkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC YY1 281 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescUsf1Pcr1xPkRep2 hESC USF1 PCR1 2 USF-1 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001532 1532 GSM803426 Myers HudsonAlpha SL1319 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescUsf1Pcr1xPkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC USF-1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescUsf1Pcr1xPkRep1 hESC USF1 PCR1 1 USF-1 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001532 1532 GSM803426 Myers HudsonAlpha SL1159 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescUsf1Pcr1xPkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC USF-1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTead4sc101184V0422111PkRep2 hESC TEAD4 V11 2 TEAD4_(SC-101184) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003214 3214 GSM1010845 Myers HudsonAlpha SL12417 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescTead4sc101184V0422111PkRep2 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC TEAD4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTead4sc101184V0422111PkRep1 hESC TEAD4 V11 1 TEAD4_(SC-101184) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003214 3214 GSM1010845 Myers HudsonAlpha SL10882 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescTead4sc101184V0422111PkRep1 None Peaks Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC TEAD4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTcf12Pcr1xPkRep2 hESC TCF12 PCR1 2 TCF12 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001531 1531 GSM803427 Myers HudsonAlpha SL1315 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescTcf12Pcr1xPkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC TCF12 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTcf12Pcr1xPkRep1 hESC TCF12 PCR1 1 TCF12 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001531 1531 GSM803427 Myers HudsonAlpha SL1158 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescTcf12Pcr1xPkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC TCF12 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf7sc101167V0416102PkRep2 hESC TAF7 V102 2 TAF7_(SC-101167) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-13 2011-09-13 wgEncodeEH001610 1610 GSM803501 Myers HudsonAlpha SL3062 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescTaf7sc101167V0416102PkRep2 None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC TAF7 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf7sc101167V0416102PkRep1 hESC TAF7 V102 1 TAF7_(SC-101167) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-13 2011-09-13 wgEncodeEH001610 1610 GSM803501 Myers HudsonAlpha SL2697 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescTaf7sc101167V0416102PkRep1 None Peaks The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC TAF7 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf1V0416102PkRep2 hESC TAF1 V102 2 TAF1 H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2009-12-17 2010-09-16 wgEncodeEH001500 1500 GSM803450 Myers HudsonAlpha SL964 v041610.2 2 exp wgEncodeHaibTfbsH1hescTaf1V0416102PkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC TAF1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescTaf1V0416102PkRep1 hESC TAF1 V102 1 TAF1 H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2009-12-17 2010-09-16 wgEncodeEH001500 1500 GSM803450 Myers HudsonAlpha SL853 v041610.2 1 exp wgEncodeHaibTfbsH1hescTaf1V0416102PkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC TAF1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSrfPcr1xPkRep2 hESC SRF PCR1 2 SRF H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001533 1533 GSM803425 Myers HudsonAlpha SL1659 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescSrfPcr1xPkRep2 None Peaks Serum response transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC SRF PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSrfPcr1xPkRep1 hESC SRF PCR1 1 SRF H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001533 1533 GSM803425 Myers HudsonAlpha SL1483 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescSrfPcr1xPkRep1 None Peaks Serum response transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC SRF PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp4v20V0422111PkRep2 hESC SP4 V11 2 SP4_(V-20) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002317 2317 GSM1010743 Myers HudsonAlpha SL8135 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescSp4v20V0422111PkRep2 None Peaks Binds to GT and GC boxes promoters elements. Probable transcriptional activator. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC SP4 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp4v20V0422111PkRep1 hESC SP4 V11 1 SP4_(V-20) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002317 2317 GSM1010743 Myers HudsonAlpha SL7836 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescSp4v20V0422111PkRep1 None Peaks Binds to GT and GC boxes promoters elements. Probable transcriptional activator. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC SP4 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp2V0422111PkRep2 hESC SP2 V11 2 SP2_(SC-643) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-07 2012-06-07 wgEncodeEH002302 2302 GSM1010776 Myers HudsonAlpha SL6005 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescSp2V0422111PkRep2 None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC SP2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp2V0422111PkRep1 hESC SP2 V11 1 SP2_(SC-643) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-07 2012-06-07 wgEncodeEH002302 2302 GSM1010776 Myers HudsonAlpha SL5690 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescSp2V0422111PkRep1 None Peaks This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors. Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs. This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC SP2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp1Pcr1xPkRep2 hESC SP1 PCR1 2 SP1 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001529 1529 GSM803377 Myers HudsonAlpha SL1318 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescSp1Pcr1xPkRep2 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC SP1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSp1Pcr1xPkRep1 hESC SP1 PCR1 1 SP1 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001529 1529 GSM803377 Myers HudsonAlpha SL1166 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescSp1Pcr1xPkRep1 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC SP1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSix5Pcr1xPkRep2 hESC SIX5 PCR1 2 SIX5 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001528 1528 GSM803405 Myers HudsonAlpha SL1317 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescSix5Pcr1xPkRep2 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC SIX5 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSix5Pcr1xPkRep1 hESC SIX5 PCR1 1 SIX5 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001528 1528 GSM803405 Myers HudsonAlpha SL1162 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescSix5Pcr1xPkRep1 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC SIX5 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSin3ak20Pcr1xPkRep2 hESC Sin3A PCR1 2 Sin3Ak-20 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001530 1530 GSM803428 Myers HudsonAlpha SL1313 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescSin3ak20Pcr1xPkRep2 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Sin3Ak-20 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescSin3ak20Pcr1xPkRep1 hESC Sin3A PCR1 1 Sin3Ak-20 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-22 2011-01-22 wgEncodeEH001530 1530 GSM803428 Myers HudsonAlpha SL1157 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescSin3ak20Pcr1xPkRep1 None Peaks Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Sin3Ak-20 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxraV0416102PkRep2 hESC RXRA V102 2 RXRA H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-13 2011-06-13 wgEncodeEH001560 1560 GSM803506 Myers HudsonAlpha SL2346 v041610.2 2 exp wgEncodeHaibTfbsH1hescRxraV0416102PkRep2 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC RXRA v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRxraV0416102PkRep1 hESC RXRA V102 1 RXRA H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-13 2011-06-13 wgEncodeEH001560 1560 GSM803506 Myers HudsonAlpha SL1163 v041610.2 1 exp wgEncodeHaibTfbsH1hescRxraV0416102PkRep1 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC RXRA v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRad21V0416102PkRep2 hESC RAD21 V102 2 Rad21 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001593 1593 GSM803466 Myers HudsonAlpha SL3066 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescRad21V0416102PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC RAD21 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescRad21V0416102PkRep1 hESC RAD21 V102 1 Rad21 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-12-08 2011-09-08 wgEncodeEH001593 1593 GSM803466 Myers HudsonAlpha SL2689 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescRad21V0416102PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC RAD21 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102PkRep2 hESC POU5F1 2 POU5F1_(SC-9081) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001636 1636 GSM803438 Myers HudsonAlpha SL3453 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102PkRep2 None Peaks This gene encodes a transcription factor containing a POU homeodomain. This transcription factor plays a role in embryonic development, especially during early embryogenesis, and it is necessary for embryonic stem cell pluripotency. A translocation of this gene with the Ewing's sarcoma gene, t(6;22)(p21;q12), has been linked to tumor formation. Alternative splicing, as well as usage of alternative translation initiation codons, results in multiple isoforms, one of which initiates at a non-AUG (CUG) start codon. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12 (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC POU5F1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102PkRep1 hESC POU5F1 1 POU5F1_(SC-9081) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001636 1636 GSM803438 Myers HudsonAlpha SL2548 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102PkRep1 None Peaks This gene encodes a transcription factor containing a POU homeodomain. This transcription factor plays a role in embryonic development, especially during early embryogenesis, and it is necessary for embryonic stem cell pluripotency. A translocation of this gene with the Ewing's sarcoma gene, t(6;22)(p21;q12), has been linked to tumor formation. Alternative splicing, as well as usage of alternative translation initiation codons, results in multiple isoforms, one of which initiates at a non-AUG (CUG) start codon. Related pseudogenes have been identified on chromosomes 1, 3, 8, 10, and 12 (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC POU5F1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol24h8V0416102PkRep2 hESC Pol2-4H8 V102 2 Pol2-4H8 H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001514 1514 GSM803484 Myers HudsonAlpha SL1051 v041610.2 2 exp wgEncodeHaibTfbsH1hescPol24h8V0416102PkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Pol2-4H8 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol24h8V0416102PkRep1 hESC Pol2-4H8 V102 1 Pol2-4H8 H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-01-06 2010-10-06 wgEncodeEH001514 1514 GSM803484 Myers HudsonAlpha SL979 v041610.2 1 exp wgEncodeHaibTfbsH1hescPol24h8V0416102PkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Pol2-4H8 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol2V0416102PkRep2 hESC Pol2 V102 2 Pol2 H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2009-12-17 2010-09-16 wgEncodeEH001499 1499 GSM803366 Myers HudsonAlpha SL1052 v041610.2 2 exp wgEncodeHaibTfbsH1hescPol2V0416102PkRep2 None Peaks RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Pol2 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescPol2V0416102PkRep1 hESC Pol2 V102 1 Pol2 H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2009-12-17 2010-09-16 wgEncodeEH001499 1499 GSM803366 Myers HudsonAlpha SL980 v041610.2 1 exp wgEncodeHaibTfbsH1hescPol2V0416102PkRep1 None Peaks RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Pol2 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescP300V0416102PkRep2 hESC p300 V102 2 p300 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-27 2011-06-27 wgEncodeEH001574 1574 GSM803542 Myers HudsonAlpha SL1883 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescP300V0416102PkRep2 None Peaks EP300(c-20) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC p300 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescP300V0416102PkRep1 hESC p300 V102 1 p300 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-27 2011-06-27 wgEncodeEH001574 1574 GSM803542 Myers HudsonAlpha SL2250 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescP300V0416102PkRep1 None Peaks EP300(c-20) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC p300 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNrsfV0416102PkRep2 hESC NRSF V102 2 NRSF H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2009-12-17 2010-09-16 wgEncodeEH001498 1498 GSM803365 Myers HudsonAlpha SL1053 v041610.2 2 exp wgEncodeHaibTfbsH1hescNrsfV0416102PkRep2 None Peaks Neuron-restrictive silencer transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC NRSF v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNrsfV0416102PkRep1 hESC NRSF V102 1 NRSF H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2009-12-17 2010-09-16 wgEncodeEH001498 1498 GSM803365 Myers HudsonAlpha SL978 v041610.2 1 exp wgEncodeHaibTfbsH1hescNrsfV0416102PkRep1 None Peaks Neuron-restrictive silencer transcription factor embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC NRSF v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNanogsc33759V0416102PkRep2 hESC NANOG V102 2 NANOG_(SC-33759) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001635 1635 GSM803437 Myers HudsonAlpha SL3068 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescNanogsc33759V0416102PkRep2 None Peaks Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes (By similarity). Acts as a transcriptional activator or repressor (By similarity). Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3' (By similarity). When overexpressed, promotes cells to enter into S phase and proliferation (By similarity) (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC NANOG v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescNanogsc33759V0416102PkRep1 hESC NANOG V102 1 NANOG_(SC-33759) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-11 2011-10-11 wgEncodeEH001635 1635 GSM803437 Myers HudsonAlpha SL2687 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescNanogsc33759V0416102PkRep1 None Peaks Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes (By similarity). Acts as a transcriptional activator or repressor (By similarity). Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'-[CG][GA][CG]C[GC]ATTAN[GC]-3' (By similarity). When overexpressed, promotes cells to enter into S phase and proliferation (By similarity) (provided by RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC NANOG v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescMaxV0422111PkRep2 hESC Max V11 2 Max H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003225 3225 GSM1010898 Myers HudsonAlpha SL13302 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescMaxV0422111PkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC Max v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescMaxV0422111PkRep1 hESC Max V11 1 Max H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003225 3225 GSM1010898 Myers HudsonAlpha SL12411 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescMaxV0422111PkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC Max v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescJundV0416102PkRep2 hESC JunD V102 2 JunD H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH001579 1579 GSM803529 Myers HudsonAlpha SL3065 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescJundV0416102PkRep2 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC JunD v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescJundV0416102PkRep1 hESC JunD V102 1 JunD H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH001579 1579 GSM803529 Myers HudsonAlpha SL2690 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescJundV0416102PkRep1 None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC JunD v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescHdac2sc6296V0416102PkRep2 hESC HDAC2 V102 2 HDAC2_(SC-6296) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2011-12-02 wgEncodeEH001659 1659 GSM803345 Myers HudsonAlpha SL3454 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescHdac2sc6296V0416102PkRep2 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC HDAC2 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescHdac2sc6296V0416102PkRep1 hESC HDAC2 V102 1 HDAC2_(SC-6296) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2011-12-02 wgEncodeEH001659 1659 GSM803345 Myers HudsonAlpha SL3935 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescHdac2sc6296V0416102PkRep1 None Peaks This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC HDAC2 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescGabpPcr1xPkRep2 hESC GABP PCR1 2 GABP H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-29 2011-01-29 wgEncodeEH001534 1534 GSM803424 Myers HudsonAlpha SL1660 hg19 PCR1x 2 exp MACS wgEncodeHaibTfbsH1hescGabpPcr1xPkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC GABP PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescGabpPcr1xPkRep1 hESC GABP PCR1 1 GABP H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-04-29 2011-01-29 wgEncodeEH001534 1534 GSM803424 Myers HudsonAlpha SL1518 hg19 PCR1x 1 exp MACS wgEncodeHaibTfbsH1hescGabpPcr1xPkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC GABP PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescFosl1sc183V0416102PkRep2 hESC FOSL1 V102 2 FOSL1_(SC-183) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001660 1660 GSM803382 Myers HudsonAlpha SL4211 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescFosl1sc183V0416102PkRep2 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC FOSL1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescFosl1sc183V0416102PkRep1 hESC FOSL1 V102 1 FOSL1_(SC-183) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2011-12-23 wgEncodeEH001660 1660 GSM803382 Myers HudsonAlpha SL2692 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescFosl1sc183V0416102PkRep1 None Peaks The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC FOSL1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescEgr1V0416102PkRep2 hESC Egr-1 V102 2 Egr-1 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-05-27 2011-02-27 wgEncodeEH001538 1538 GSM803430 Myers HudsonAlpha SL1885 hg19 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescEgr1V0416102PkRep2 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Egr-1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescEgr1V0416102PkRep1 hESC Egr-1 V102 1 Egr-1 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-05-27 2011-02-27 wgEncodeEH001538 1538 GSM803430 Myers HudsonAlpha SL1482 hg19 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescEgr1V0416102PkRep1 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC Egr-1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescE2f6V0422111PkRep2 hESC E2F6 V11 2 E2F6 H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003224 3224 GSM1010899 Myers HudsonAlpha SL13304 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescE2f6V0422111PkRep2 None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC E2F6 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescE2f6V0422111PkRep1 hESC E2F6 V11 1 E2F6 H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-03 2013-04-03 wgEncodeEH003224 3224 GSM1010899 Myers HudsonAlpha SL12414 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescE2f6V0422111PkRep1 None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC E2F6 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCtcfsc5916V0416102PkRep2 hESC CTCF V102 2 CTCF_(SC-5916) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001649 1649 GSM803419 Myers HudsonAlpha SL3067 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescCtcfsc5916V0416102PkRep2 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC CTCF 5916 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCtcfsc5916V0416102PkRep1 hESC CTCF V102 1 CTCF_(SC-5916) H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001649 1649 GSM803419 Myers HudsonAlpha SL2688 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescCtcfsc5916V0416102PkRep1 None Peaks This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC CTCF 5916 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCreb1sc240V0422111PkRep2 hESC CREB1 V11 2 CREB1_(SC-240) H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003229 3229 GSM1010896 Myers HudsonAlpha SL13303 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescCreb1sc240V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC CREB1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescCreb1sc240V0422111PkRep1 hESC CREB1 V11 1 CREB1_(SC-240) H1-hESC ChipSeq ENCODE Jul 2012 Freeze 2012-07-16 2013-04-16 wgEncodeEH003229 3229 GSM1010896 Myers HudsonAlpha SL12413 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescCreb1sc240V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC CREB1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescBcl11aV0416102PkRep2 hESC BCL V102 2 BCL11A H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-01-05 2011-10-05 wgEncodeEH001625 1625 GSM803476 Myers HudsonAlpha SL3989 v041610.2 2 exp wgEncodeHaibTfbsH1hescBcl11aV0416102PkRep2 None Peaks This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC BCL11A v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescBcl11aPcr1xPkRep1 hESC BCL PCR1 1 BCL11A H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-03-02 2010-04-22 2011-01-22 wgEncodeEH001527 1527 GSM803396 Myers HudsonAlpha SL1314 PCR1x 1 exp wgEncodeHaibTfbsH1hescBcl11aPcr1xPkRep1 None Peaks This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC BCL11A PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf3V0416102PkRep2 hESC ATF3 V102 2 ATF3 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001566 1566 GSM803512 Myers HudsonAlpha SL1968 v041610.2 2 exp MACS wgEncodeHaibTfbsH1hescAtf3V0416102PkRep2 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC ATF3 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf3V0416102PkRep1 hESC ATF3 V102 1 ATF3 H1-hESC ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001566 1566 GSM803512 Myers HudsonAlpha SL1519 v041610.2 1 exp MACS wgEncodeHaibTfbsH1hescAtf3V0416102PkRep1 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment H1-hESC ATF3 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf2sc81188V0422111PkRep2 hESC ATF2 V11 2 ATF2_(SC-81188) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002316 2316 GSM1010742 Myers HudsonAlpha SL8136 v042211.1 2 exp MACS wgEncodeHaibTfbsH1hescAtf2sc81188V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC ATF2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsH1hescAtf2sc81188V0422111PkRep1 hESC ATF2 V11 1 ATF2_(SC-81188) H1-hESC ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002316 2316 GSM1010742 Myers HudsonAlpha SL7904 v042211.1 1 exp MACS wgEncodeHaibTfbsH1hescAtf2sc81188V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) embryonic stem cells Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment H1-hESC ATF2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102PkRep2 GM78 ZEB1 V102 2 ZEB1_(SC-25388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001645 1645 GSM803411 Myers HudsonAlpha SL3254 v041610.2 2 exp MACS wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102PkRep2 None Peaks This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ZEB1 v041610.2 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102PkRep1 GM78 ZEB1 V102 1 ZEB1_(SC-25388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001645 1645 GSM803411 Myers HudsonAlpha SL2957 v041610.2 1 exp MACS wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102PkRep1 None Peaks This gene encodes a zinc finger transcription factor. The encoded protein likely plays a role in transcriptional repression of interleukin 2. Mutations in this gene have ben associated with posterior polymorphous corneal dystrophy-3 and late-onset Fuchs endothelial corneal dystrophy. Alternatively spliced transcript variants encoding different isoforms have been described. (provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ZEB1 v041610.2 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zbtb33Pcr1xPkRep2 GM78 ZBTB33 2 ZBTB33 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-11-30 2010-08-30 wgEncodeEH001488 1488 GSM803392 Myers HudsonAlpha SL923 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Zbtb33Pcr1xPkRep2 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ZBTB33 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Zbtb33Pcr1xPkRep1 GM78 ZBTB33 1 ZBTB33 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-11-30 2010-08-30 wgEncodeEH001488 1488 GSM803392 Myers HudsonAlpha SL814 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Zbtb33Pcr1xPkRep1 None Peaks KAISO is a transcriptional regulator that binds, via its zinc fingers, to DNA sequences containing methylated CGCG or to the consensus KAISO-binding site (KBS) TCCTGCNA B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ZBTB33 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xPkRep2 GM78 YY1 PCR1 2 YY1_(SC-281) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-15 2011-11-15 wgEncodeEH001657 1657 GSM803406 Myers HudsonAlpha SL2129 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xPkRep2 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 YY1 281 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xPkRep1 GM78 YY1 PCR1 1 YY1_(SC-281) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-15 2011-11-15 wgEncodeEH001657 1657 GSM803406 Myers HudsonAlpha SL1475 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Yy1sc281Pcr1xPkRep1 None Peaks YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 YY1 281 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Usf1Pcr2xPkRep2 GM78 USF1 PCR2 2 USF-1 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2009-07-02 2010-04-01 wgEncodeEH001468 1468 GSM803347 Myers HudsonAlpha SL483 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsGm12878Usf1Pcr2xPkRep2 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 USF-1 PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Usf1Pcr2xPkRep1 GM78 USF1 PCR2 1 USF-1 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2009-07-02 2010-04-01 wgEncodeEH001468 1468 GSM803347 Myers HudsonAlpha SL448 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsGm12878Usf1Pcr2xPkRep1 None Peaks The ubiquitously expressed cellular upstream stimulatory factor (USF) consists of USF-1 and USF-2 polypeptides which independently exhibit site-specific DNA binding and are members of the c-Myc-related family of regulatory factors containing helix-loop-helix domains. USF also contains a leucine repeat that is required for efficient DNA binding. USF was originally identified as an up- stream stimulatory factor that binds the core sequence CACGTG in the adeno- virus late promoter. These findings, together with the demonstration of coop- erative interaction between USF and the initiator-binding protein, TFII-I, raises the possibility of a more general involvement of USF in transcriptional regula- tion. While expression of both USF-1 and USF-2 species is ubiquitous, different ratios of USF homo- and heterodimers are found in different cell types. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 USF-1 PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf3Pcr1xPkRep2 GM78 TCF3 PCR1 2 TCF3_(SC-349) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002315 2315 GSM1010745 Myers HudsonAlpha SL633 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Tcf3Pcr1xPkRep2 None Peaks Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 TCF3 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf3Pcr1xPkRep1 GM78 TCF3 PCR1 1 TCF3_(SC-349) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002315 2315 GSM1010745 Myers HudsonAlpha SL480 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Tcf3Pcr1xPkRep1 None Peaks Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 TCF3 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf12Pcr1xPkRep2 GM78 TCF12 PCR1 2 TCF12 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-29 2010-07-29 wgEncodeEH001485 1485 GSM803389 Myers HudsonAlpha SL1019 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Tcf12Pcr1xPkRep2 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 TCF12 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Tcf12Pcr1xPkRep1 GM78 TCF12 PCR1 1 TCF12 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-27 2010-07-27 wgEncodeEH001485 1485 GSM803389 Myers HudsonAlpha SL673 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Tcf12Pcr1xPkRep1 None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 TCF12 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Taf1Pcr1xPkRep2 GM78 TAF1 PCR1 2 TAF1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-04-18 2009-10-29 2010-07-29 wgEncodeEH001478 1478 GSM803537 Myers HudsonAlpha SL1062 PCR1x 2 exp wgEncodeHaibTfbsGm12878Taf1Pcr1xPkRep2 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 TAF1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Taf1Pcr1xPkRep1 GM78 TAF1 PCR1 1 TAF1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-23 2009-07-20 2010-04-20 wgEncodeEH001478 1478 GSM803537 Myers HudsonAlpha SL805 PCR1x 1 exp wgEncodeHaibTfbsGm12878Taf1Pcr1xPkRep1 None Peaks TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 TAF1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Stat5asc74442V0422111PkRep2 GM78 STAT5A V11 2 STAT5A_(SC-74442) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002321 2321 GSM1010721 Myers HudsonAlpha SL8127 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Stat5asc74442V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 STAT5A v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Stat5asc74442V0422111PkRep1 GM78 STAT5A V11 1 STAT5A_(SC-74442) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002321 2321 GSM1010721 Myers HudsonAlpha SL7897 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Stat5asc74442V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis. The mouse counterpart of this gene is found to induce the expression of BCL2L1/BCL-X(L), which suggests the antiapoptotic function of this gene in cells. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 STAT5A v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfV0416101PkRep2 GM78 SRF V101 2 SRF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001624 1624 GSM803477 Myers HudsonAlpha SL3827 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878SrfV0416101PkRep2 None Peaks Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 SRF v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfV0416101PkRep1 GM78 SRF V101 1 SRF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-05 2011-10-05 wgEncodeEH001624 1624 GSM803477 Myers HudsonAlpha SL3578 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878SrfV0416101PkRep1 None Peaks Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 SRF v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfPcr2xPkRep2 GM78 SRF PCR2 2 SRF GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-20 2009-08-20 wgEncodeEH001464 1464 GSM803350 Myers HudsonAlpha SL292 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsGm12878SrfPcr2xPkRep2 None Peaks Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 SRF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878SrfPcr2xPkRep1 GM78 SRF PCR2 1 SRF GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-20 2009-08-20 wgEncodeEH001464 1464 GSM803350 Myers HudsonAlpha SL291 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsGm12878SrfPcr2xPkRep1 None Peaks Serum response transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 SRF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Sp1Pcr1xPkRep2 GM78 SP1 PCR1 2 SP1 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-17 2010-09-16 wgEncodeEH001496 1496 GSM803363 Myers HudsonAlpha SL846 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Sp1Pcr1xPkRep2 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 SP1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Sp1Pcr1xPkRep1 GM78 SP1 PCR1 1 SP1 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-17 2010-09-16 wgEncodeEH001496 1496 GSM803363 Myers HudsonAlpha SL746 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Sp1Pcr1xPkRep1 None Peaks SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 SP1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Six5Pcr1xPkRep2 GM78 SIX5 PCR1 2 SIX5 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-06-07 2011-03-07 wgEncodeEH001542 1542 GSM803338 Myers HudsonAlpha SL1200 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Six5Pcr1xPkRep2 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 SIX5 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Six5Pcr1xPkRep1 GM78 SIX5 PCR1 1 SIX5 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-06-07 2011-03-07 wgEncodeEH001542 1542 GSM803338 Myers HudsonAlpha SL1061 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Six5Pcr1xPkRep1 None Peaks The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 SIX5 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxraPcr1xPkRep2 GM78 RXRA PCR1 2 RXRA GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001541 1541 GSM803341 Myers HudsonAlpha SL1265 PCR1x 2 exp wgEncodeHaibTfbsGm12878RxraPcr1xPkRep2 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 RXRA PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878RxraPcr1xPkRep1 GM78 RXRA PCR1 1 RXRA GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-07 2011-03-07 wgEncodeEH001541 1541 GSM803341 Myers HudsonAlpha SL1063 PCR1x 1 exp wgEncodeHaibTfbsGm12878RxraPcr1xPkRep1 None Peaks Retinoid X receptors (RXRs) and retinoic acid receptors (RARs), are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors exert their action by binding, as homodimers or heterodimers, to specific sequences in the promoters of target genes and regulating their transcription. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 RXRA PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Runx3sc101553V0422111PkRep2 GM78 RUNX3 V11 2 RUNX3_(SC-101553) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002330 2330 GSM1010893 Myers HudsonAlpha SL8128 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Runx3sc101553V0422111PkRep2 None Peaks This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Multiple transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 RUNX3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Runx3sc101553V0422111PkRep1 GM78 RUNX3 V11 1 RUNX3_(SC-101553) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002330 2330 GSM1010893 Myers HudsonAlpha SL7898 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Runx3sc101553V0422111PkRep1 None Peaks This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Multiple transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 RUNX3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Rad21V0416101PkRep2 GM78 RAD21 V101 2 Rad21 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001640 1640 GSM803416 Myers HudsonAlpha SL3934 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878Rad21V0416101PkRep2 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 RAD21 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Rad21V0416101PkRep1 GM78 RAD21 V101 1 Rad21 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001640 1640 GSM803416 Myers HudsonAlpha SL3933 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878Rad21V0416101PkRep1 None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 RAD21 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pu1Pcr1xPkRep3 GM78 PU.1 PCR1 3 PU.1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH001476 1476 GSM803531 Myers HudsonAlpha SL963 PCR1x 3 exp MACS wgEncodeHaibTfbsGm12878Pu1Pcr1xPkRep3 None Peaks PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PU.1 PCR1x ChIP-seq Peaks Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pu1Pcr1xPkRep2 GM78 PU.1 PCR1 2 PU.1 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-20 2010-04-20 wgEncodeEH001476 1476 GSM803531 Myers HudsonAlpha SL649 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Pu1Pcr1xPkRep2 None Peaks PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PU.1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pu1Pcr1xPkRep1 GM78 PU.1 PCR1 1 PU.1 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-20 2010-04-20 wgEncodeEH001476 1476 GSM803531 Myers HudsonAlpha SL612 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Pu1Pcr1xPkRep1 None Peaks PU.1 (H-135) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PU.1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pou2f2Pcr1xPkRep3 GM78 POU2F2 3 POU2F2 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH001475 1475 GSM803534 Myers HudsonAlpha SL851 PCR1x 3 exp MACS wgEncodeHaibTfbsGm12878Pou2f2Pcr1xPkRep3 None Peaks Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 POU2F2 PCR1x ChIP-seq Peaks Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pou2f2Pcr1xPkRep2 GM78 POU2F2 2 POU2F2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-20 2010-04-20 wgEncodeEH001475 1475 GSM803534 Myers HudsonAlpha SL648 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Pou2f2Pcr1xPkRep2 None Peaks Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 POU2F2 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pou2f2Pcr1xPkRep1 GM78 POU2F2 1 POU2F2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-20 2010-04-20 wgEncodeEH001475 1475 GSM803534 Myers HudsonAlpha SL614 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Pou2f2Pcr1xPkRep1 None Peaks Transcription factor that specifically binds to the octamer motif (5'-ATTTGCAT-3'). Regulates transcription in a number of tissues in addition to activating immunoglobulin gene expression. Modulates transcription transactivation by NR3C1, AR and PGR. Isoform 5 activates the U2 small nuclear RNA (snRNA) promoter. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 POU2F2 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol24h8Pcr1xPkRep2 GM78 Pol2-4H8 PCR1 2 Pol2-4H8 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-08 2010-10-08 wgEncodeEH001517 1517 GSM803485 Myers HudsonAlpha SL847 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Pol24h8Pcr1xPkRep2 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 Pol2-4H8 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol24h8Pcr1xPkRep1 GM78 Pol2-4H8 PCR1 1 Pol2-4H8 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-01-08 2010-10-08 wgEncodeEH001517 1517 GSM803485 Myers HudsonAlpha SL748 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Pol24h8Pcr1xPkRep1 None Peaks This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 Pol2-4H8 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol2Pcr2xPkRep2 GM78 Pol2 PCR2 2 Pol2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-20 2009-08-20 wgEncodeEH001463 1463 GSM803355 Myers HudsonAlpha SL209 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsGm12878Pol2Pcr2xPkRep2 None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 Pol2 PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pol2Pcr2xPkRep1 GM78 Pol2 PCR2 1 Pol2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-20 2009-08-20 wgEncodeEH001463 1463 GSM803355 Myers HudsonAlpha SL207 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsGm12878Pol2Pcr2xPkRep1 None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 Pol2 PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep2 GM78 PML V11 2 PML_(SC-71910) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002308 2308 GSM1010771 Myers HudsonAlpha SL7831 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep2 None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 PML v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep1 GM78 PML V11 1 PML_(SC-71910) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002308 2308 GSM1010771 Myers HudsonAlpha SL7281 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Pmlsc71910V0422111PkRep1 None Peaks The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 PML v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pbx3Pcr1xPkRep2 GM78 PBx3 PCR1 2 Pbx3 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-20 2010-04-20 wgEncodeEH001477 1477 GSM803532 Myers HudsonAlpha SL647 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Pbx3Pcr1xPkRep2 None Peaks Pbx 3 (D-17) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PBx3 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pbx3Pcr1xPkRep1 GM78 PBx3 PCR1 1 Pbx3 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-07-20 2010-04-20 wgEncodeEH001477 1477 GSM803532 Myers HudsonAlpha SL615 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Pbx3Pcr1xPkRep1 None Peaks Pbx 3 (D-17) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PBx3 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5n19Pcr1xPkRep2 GM78 PAX5 PCR1 2 PAX5-N19 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-17 2010-09-17 wgEncodeEH001495 1495 GSM803362 Myers HudsonAlpha SL848 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Pax5n19Pcr1xPkRep2 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PAX5-N19 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5n19Pcr1xPkRep1 GM78 PAX5 PCR1 1 PAX5-N19 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-17 2010-09-17 wgEncodeEH001495 1495 GSM803362 Myers HudsonAlpha SL677 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Pax5n19Pcr1xPkRep1 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PAX5-N19 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5c20Pcr1xPkRep2 GM78 PAX5 PCR1 2 PAX5-C20 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-04 2010-09-04 wgEncodeEH001489 1489 GSM803391 Myers HudsonAlpha SL735 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Pax5c20Pcr1xPkRep2 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PAX5-C20 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Pax5c20Pcr1xPkRep1 GM78 PAX5 PCR1 1 PAX5-C20 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-12-04 2010-09-04 wgEncodeEH001489 1489 GSM803391 Myers HudsonAlpha SL675 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Pax5c20Pcr1xPkRep1 None Peaks This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 PAX5-C20 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878P300Pcr1xPkRep2 GM78 p300 PCR1 2 p300 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-11-25 2010-08-25 wgEncodeEH001487 1487 GSM803387 Myers HudsonAlpha SL564 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878P300Pcr1xPkRep2 None Peaks EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 p300 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878P300Pcr1xPkRep1 GM78 p300 PCR1 1 p300 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-11-25 2010-08-25 wgEncodeEH001487 1487 GSM803387 Myers HudsonAlpha SL551 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878P300Pcr1xPkRep1 None Peaks EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 p300 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep2 GM78 NRSF PCR2 2 NRSF GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-25 2009-08-25 wgEncodeEH001465 1465 GSM803349 Myers HudsonAlpha SL204 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep2 None Peaks Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 NRSF PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep1 GM78 NRSF PCR2 1 NRSF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-08-06 2008-11-25 2011-05-06 wgEncodeEH001465 1465 GSM803349 Myers HudsonAlpha SL202 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep1 None Peaks Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 NRSF PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr1xPkRep2 GM78 NRSF PCR1 2 NRSF GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002314 2314 GSM1010744 Myers HudsonAlpha SL7333 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878NrsfPcr1xPkRep2 None Peaks Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 NRSF PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878NrsfPcr1xPkRep1 GM78 NRSF PCR1 1 NRSF GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEH002314 2314 GSM1010744 Myers HudsonAlpha SL852 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878NrsfPcr1xPkRep1 None Peaks Neuron-restrictive silencer transcription factor B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 NRSF PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep2 GM78 NFIC V11 2 NFIC_(SC-81335) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002343 2343 GSM1010881 Myers HudsonAlpha SL8392 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep2 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 NFIC v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep1 GM78 NFIC V11 1 NFIC_(SC-81335) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-08 2012-09-08 wgEncodeEH002343 2343 GSM1010881 Myers HudsonAlpha SL8083 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Nficsc81335V0422111PkRep1 None Peaks Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 NFIC v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep2 GM78 NFATC1 V11 2 NFATC1_(SC-17834) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002307 2307 GSM1010779 Myers HudsonAlpha SL7830 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep2 None Peaks The product of this gene is a component of the nuclear factor of activated T cells DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation, and an inducible nuclear component. Proteins belonging to this family of transcription factors play a central role in inducible gene transcription during immune response. The product of this gene is an inducible nuclear component. It functions as a major molecular target for the immunosuppressive drugs such as cyclosporin A. Five transcript variants encoding distinct isoforms have been identified for this gene. Different isoforms of this protein may regulate inducible expression of different cytokine genes. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 NFATC1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep1 GM78 NFATC1 V11 1 NFATC1_(SC-17834) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002307 2307 GSM1010779 Myers HudsonAlpha SL7280 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep1 None Peaks The product of this gene is a component of the nuclear factor of activated T cells DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation, and an inducible nuclear component. Proteins belonging to this family of transcription factors play a central role in inducible gene transcription during immune response. The product of this gene is an inducible nuclear component. It functions as a major molecular target for the immunosuppressive drugs such as cyclosporin A. Five transcript variants encoding distinct isoforms have been identified for this gene. Different isoforms of this protein may regulate inducible expression of different cytokine genes. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 NFATC1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep2 GM78 MTA3 V11 2 MTA3_(SC-81325) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002329 2329 GSM1010729 Myers HudsonAlpha SL8129 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep2 None Peaks Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 MTA3 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep1 GM78 MTA3 V11 1 MTA3_(SC-81325) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002329 2329 GSM1010729 Myers HudsonAlpha SL7899 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Mta3sc81325V0422111PkRep1 None Peaks Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 MTA3 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2csc13268V0416101PkRep2 GM78 MEFC V101 2 MEF2C_(SC-13268) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001648 1648 GSM803420 Myers HudsonAlpha SL2127 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878Mef2csc13268V0416101PkRep2 None Peaks This locus encodes a member of the MADS box transcription enhancer factor 2 (MEF2) family of proteins, which play a role in myogenesis. The encoded protein, MEF2 polypeptide C, has both trans-activating and DNA binding activities. This protein may play a role in maintaining the differentiated state of muscle cells. Mutations and deletions at this locus have been associated with severe mental retardation, stereotypic movements, epilepsy, and cerebral malformation. Alternatively spliced transcript variants have been described. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 MEF2C v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2csc13268V0416101PkRep1 GM78 MEFC V101 1 MEF2C_(SC-13268) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-21 wgEncodeEH001648 1648 GSM803420 Myers HudsonAlpha SL1654 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878Mef2csc13268V0416101PkRep1 None Peaks This locus encodes a member of the MADS box transcription enhancer factor 2 (MEF2) family of proteins, which play a role in myogenesis. The encoded protein, MEF2 polypeptide C, has both trans-activating and DNA binding activities. This protein may play a role in maintaining the differentiated state of muscle cells. Mutations and deletions at this locus have been associated with severe mental retardation, stereotypic movements, epilepsy, and cerebral malformation. Alternatively spliced transcript variants have been described. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 MEF2C v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2aPcr1xPkRep2 GM78 MEF2A PCR1 2 MEF2A GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001565 1565 GSM803511 Myers HudsonAlpha SL1792 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Mef2aPcr1xPkRep2 None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 MEF2A PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Mef2aPcr1xPkRep1 GM78 MEF2A PCR1 1 MEF2A GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001565 1565 GSM803511 Myers HudsonAlpha SL1425 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Mef2aPcr1xPkRep1 None Peaks The protein encoded by this gene is a DNA-binding transcription factor that activates many muscme-specific, growth factor-induced, and stress-induced genes. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 MEF2A PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xPkRep2 GM78 IRF4 PCR1 2 IRF4_(SC-6059) GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-29 2010-07-29 wgEncodeEH001484 1484 GSM803390 Myers HudsonAlpha SL951 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xPkRep2 None Peaks The protein encoded by this gene belongs to the IRF (interferon regulatory factor) family. It functions as a lymphocyte specific transcription factor and negatively regulates TLR signaling by selectively competing with IRF5. A chromosomal translocation involving this gene and the IgH locus, t(6;14)(p25;q32), may be a cause of multiple myeloma (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 IRF4 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xPkRep1 GM78 IRF4 PCR1 1 IRF4_(SC-6059) GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-27 2010-07-27 wgEncodeEH001484 1484 GSM803390 Myers HudsonAlpha SL838 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xPkRep1 None Peaks The protein encoded by this gene belongs to the IRF (interferon regulatory factor) family. It functions as a lymphocyte specific transcription factor and negatively regulates TLR signaling by selectively competing with IRF5. A chromosomal translocation involving this gene and the IgH locus, t(6;14)(p25;q32), may be a cause of multiple myeloma (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 IRF4 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878GabpPcr2xPkRep2 GM78 GABP PCR2 2 GABP GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-20 2009-08-20 wgEncodeEH001462 1462 GSM803356 Myers HudsonAlpha SL205 hg18 PCR2x 2 exp MACS wgEncodeHaibTfbsGm12878GabpPcr2xPkRep2 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 GABP PCR2x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878GabpPcr2xPkRep1 GM78 GABP PCR2 1 GABP GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-21 2008-11-20 2009-08-20 wgEncodeEH001462 1462 GSM803356 Myers HudsonAlpha SL203 hg18 PCR2x 1 exp MACS wgEncodeHaibTfbsGm12878GabpPcr2xPkRep1 None Peaks The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 GABP PCR2x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Foxm1sc502V0422111PkRep2 GM78 FOXM1 V11 2 FOXM1_(SC-502) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002529 2529 GSM1010731 Myers HudsonAlpha SL7834 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Foxm1sc502V0422111PkRep2 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 FOXM1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Foxm1sc502V0422111PkRep1 GM78 FOXM1 V11 1 FOXM1_(SC-502) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEH002529 2529 GSM1010731 Myers HudsonAlpha SL7551 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Foxm1sc502V0422111PkRep1 None Peaks The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 FOXM1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ets1Pcr1xPkRep2V2 GM78 ETS1 PCR1 2 ETS1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH001564 1564 GSM803510 Myers HudsonAlpha SL1655 PCR1x 2 exp wgEncodeHaibTfbsGm12878Ets1Pcr1xPkRep2V2 None Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ETS1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ets1Pcr1xPkRep1V2 GM78 ETS1 PCR1 1 ETS1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEH001564 1564 GSM803510 Myers HudsonAlpha SL1507 PCR1x 1 exp wgEncodeHaibTfbsGm12878Ets1Pcr1xPkRep1V2 None Peaks ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ETS1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Elf1sc631V0416101PkRep2 GM78 ELF1 V101 2 ELF1_(SC-631) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001617 1617 GSM803496 Myers HudsonAlpha SL3352 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878Elf1sc631V0416101PkRep2 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ELF1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Elf1sc631V0416101PkRep1 GM78 ELF1 V101 1 ELF1_(SC-631) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-12-22 2011-09-22 wgEncodeEH001617 1617 GSM803496 Myers HudsonAlpha SL2253 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878Elf1sc631V0416101PkRep1 None Peaks This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ELF1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Egr1V0416101PkRep2 GM78 Egr-1 V101 2 Egr-1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001632 1632 GSM803434 Myers HudsonAlpha SL3828 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878Egr1V0416101PkRep2 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 Egr-1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Egr1V0416101PkRep1 GM78 Egr-1 V101 1 Egr-1 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2011-01-06 2011-10-06 wgEncodeEH001632 1632 GSM803434 Myers HudsonAlpha SL3579 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878Egr1V0416101PkRep1 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 Egr-1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Egr1Pcr2xPkRep3 GM78 Egr-1 PCR2 3 Egr-1 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 2012-06-30 wgEncodeEH002328 2328 GSM1010730 Myers HudsonAlpha SL482 PCR2x 3 exp MACS wgEncodeHaibTfbsGm12878Egr1Pcr2xPkRep3 None Peaks Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Regions of enriched signal in experiment GM12878 Egr-1 PCR2x ChIP-seq Peaks Rep 3 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ebfsc137065Pcr1xPkRep2 GM78 EBF1 PCR1 2 EBF1_(SC-137065) GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001480 1480 GSM803386 Myers HudsonAlpha SL988 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Ebfsc137065Pcr1xPkRep2 None Peaks Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 EBF1 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Ebfsc137065Pcr1xPkRep1 GM78 EBF1 PCR1 1 EBF1_(SC-137065) GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001480 1480 GSM803386 Myers HudsonAlpha SL745 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Ebfsc137065Pcr1xPkRep1 None Peaks Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 EBF1 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Creb1sc240V0422111PkRep2 GM78 CREB1 V11 2 CREB1_(SC-240) GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003275 3275 GSM1010760 Myers HudsonAlpha SL16741 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Creb1sc240V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 CREB1 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Creb1sc240V0422111PkRep1 GM78 CREB1 V11 1 CREB1_(SC-240) GM12878 ChipSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEH003275 3275 GSM1010760 Myers HudsonAlpha SL12408 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Creb1sc240V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in two transcript variants encoding different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 CREB1 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Cebpbsc150V0422111PkRep2 GM78 CEBPB V11 2 CEBPB_(SC-150) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003212 3212 GSM1010850 Myers HudsonAlpha SL9542 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Cebpbsc150V0422111PkRep2 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 CEBPB v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Cebpbsc150V0422111PkRep1 GM78 CEBPB V11 1 CEBPB_(SC-150) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH003212 3212 GSM1010850 Myers HudsonAlpha SL8084 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Cebpbsc150V0422111PkRep1 None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 CEBPB v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bclaf101388V0416101PkRep2 GM78 BCLAF1 2 BCLAF1_(SC-101388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001563 1563 GSM803509 Myers HudsonAlpha SL2128 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878Bclaf101388V0416101PkRep2 None Peaks This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BCLAF1 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bclaf101388V0416101PkRep1 GM78 BCLAF1 1 BCLAF1_(SC-101388) GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001563 1563 GSM803509 Myers HudsonAlpha SL1509 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878Bclaf101388V0416101PkRep1 None Peaks This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BCLAF1 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl3V0416101PkRep2 GM78 BCL3 V101 2 BCL3 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH001658 1658 GSM803342 Myers HudsonAlpha SL3931 v041610.1 2 exp MACS wgEncodeHaibTfbsGm12878Bcl3V0416101PkRep2 None Peaks This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BCL3 v041610.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl3V0416101PkRep1 GM78 BCL3 V101 1 BCL3 GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-02-18 2011-11-18 wgEncodeEH001658 1658 GSM803342 Myers HudsonAlpha SL3728 v041610.1 1 exp MACS wgEncodeHaibTfbsGm12878Bcl3V0416101PkRep1 None Peaks This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. (Provided by RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology 2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BCL3 v041610.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl11aPcr1xPkRep2 GM78 BCL PCR1 2 BCL11A GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-11-25 2010-08-25 wgEncodeEH001486 1486 GSM803388 Myers HudsonAlpha SL976 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Bcl11aPcr1xPkRep2 None Peaks This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BCL11A PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Bcl11aPcr1xPkRep1 GM78 BCL PCR1 1 BCL11A GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-11-25 2010-08-25 wgEncodeEH001486 1486 GSM803388 Myers HudsonAlpha SL650 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Bcl11aPcr1xPkRep1 None Peaks This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. Functions as a myeloid and B-cell proto-oncogene. May play important roles in leukemogenesis and hematopoiesis. An essential factor in lymphopoiesis,is required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BCL11A PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878BatfPcr1xPkRep2 GM78 BATF PCR1 2 BATF GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001479 1479 GSM803538 Myers HudsonAlpha SL985 hg18 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878BatfPcr1xPkRep2 None Peaks The protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BATF PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878BatfPcr1xPkRep1 GM78 BATF PCR1 1 BATF GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-10-26 2010-07-26 wgEncodeEH001479 1479 GSM803538 Myers HudsonAlpha SL839 hg18 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878BatfPcr1xPkRep1 None Peaks The protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 BATF PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf3Pcr1xPkRep2 GM78 ATF3 PCR1 2 ATF3 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001562 1562 GSM803508 Myers HudsonAlpha SL1508 PCR1x 2 exp MACS wgEncodeHaibTfbsGm12878Atf3Pcr1xPkRep2 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ATF3 PCR1x ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf3Pcr1xPkRep1 GM78 ATF3 PCR1 1 ATF3 GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-09-15 2011-06-15 wgEncodeEH001562 1562 GSM803508 Myers HudsonAlpha SL1269 PCR1x 1 exp MACS wgEncodeHaibTfbsGm12878Atf3Pcr1xPkRep1 None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology one 15-cycle round of PCR (Myers) Regions of enriched signal in experiment GM12878 ATF3 PCR1x ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf2sc81188V0422111PkRep2 GM78 ATF2 V11 2 ATF2_(SC-81188) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002306 2306 GSM1010780 Myers HudsonAlpha SL7561 v042211.1 2 exp MACS wgEncodeHaibTfbsGm12878Atf2sc81188V0422111PkRep2 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 ATF2 v042211.1 ChIP-seq Peaks Rep 2 from ENCODE/HAIB Regulation 
wgEncodeHaibTfbsGm12878Atf2sc81188V0422111PkRep1 GM78 ATF2 V11 1 ATF2_(SC-81188) GM12878 ChipSeq ENCODE Mar 2012 Freeze 2011-09-13 2012-06-13 wgEncodeEH002306 2306 GSM1010780 Myers HudsonAlpha SL7282 v042211.1 1 exp MACS wgEncodeHaibTfbsGm12878Atf2sc81188V0422111PkRep1 None Peaks This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds to the cAMP-responsive element (CRE), an octameric palindrome. The protein forms a homodimer or heterodimer with c-Jun and stimulates CRE-dependent transcription. The protein is also a histone acetyltransferase (HAT) that specifically acetylates histones H2B and H4 in vitro; thus it may represent a class of sequence-specific factors that activate transcription by direct effects on chromatin components. Additional transcript variants have been identified but their biological validity has not been determined. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Myers Myers - Hudson Alpha Institute for Biotechnology Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers) Regions of enriched signal in experiment GM12878 ATF2 v042211.1 ChIP-seq Peaks Rep 1 from ENCODE/HAIB Regulation 
wgEncodeSunyAlbanyGeneSt SUNY RIP GeneST GSE31724 RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany Regulation Description This track is produced as part of the ENCODE Project. This track displays transcriptional fragments associated with RNA binding proteins in different cell lines using RIP-Chip (Ribonomic) profiling on Affymetrix GeneChip&reg; Human Gene 1.0 ST Arrays. These sutracks show the genomic location of transcripts associated with the array probes. Data for this track was produced as part of the Encyclopedia of DNA Elements (ENCODE) Project. In eukaryotic organisms, gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show the associated mRNAs that co-precipitate with the targeted RNA-binding proteins using RIP-Chip profiling. Display Conventions and Configuration This track has multiple subtracks that display individually in the browser. The subtracks within this track correspond to different antibodies/target proteins tested in different cell lines. These subtracks show the genomic location of the mRNA transcripts associated with RNA Binding Proteins as determined by the Affymetrix GeneChip&reg; Human Gene 1.0 ST Array probes. Items are shaded by p-value using the formula (maxPossibleScore-((maxPossibleScore/cutOffValue)*pValue)) so that items with more significant expression levels are shaded darker. The p-values are displayed in the browser convention as -log10(pValue). Methods RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols. Antibodies specific to the RNA Binding Protein (RBP) in question were first coated onto protein A/G containing magnetic beads and then used to immunoprecipitate the targeted, endogenously-formed mRNP complexes. Antibody-coated beads were incubated/tumbled with cell lysate overnight in the cold followed by extensive rinsing and subsequent purification of associated RNA using Phenol/Chloroform extraction and ethanol precipitation. The associated transcripts were identified using GeneChip&reg; Human Gene 1.0 ST Arrays. Arrays were analyzed using Agilent's GeneSpringGX software (version 11.0). Arrays were analyzed a group at a time by applying the Iterative PLIER16 algorithm using quantile normalization. Probesets whose normalized expression levels (signal value) fell within the 18 to 98 percentile in at least two of the three replicates were retained for further analysis. A TTest (T7-Tag and RIP-Input) or a one-way ANOVA (samples and controls) was applied to these probesets and a p-value cutoff of .05 was applied. The Benjamini-Hochberg false discovery rate algorithm was then applied to generate corrected p-values, also known as q-values. The RIP-Input was summarized first and selected probesets were retained for further analysis. Next, the arrays for T7Tag (background/negative control) RIPs were summarized with those retained RIP-input probesets. Probesets that fit the above criteria for either group (RIP-Input or T7Tag) were then filtered for those that showed a minimum 2 fold increase of expression in T7Tag versus RIP-Input. Finally, arrays for treatment RIP samples were summarized together with those for RIP-inputs and T7Tag RIPs. Probesets that fit the above criteria for any group (RIP-Input or T7Tag or samples) were then filtered for probesets that showed a minimum 2 fold increase of expression in treatment over total. A similar list was produced for probesets showing the same enrichment in the T7Tag RIP set. Probesets which appeared in both treatment and negative control at these cutoff stringencies were subtracted from the treatment results as background noise, yielding the final data track. Verification All experiments (including controls) were performed in and analyzed as triplicates. Release Notes Release 2 (September 2011) of this track corrects the scores and the calculated P and Q values. In this release, the calculated P and Q values are -log10(P) and -log10(Q), and the scores, and therefore the shading of items, reflect the p-values as described in the Display Conventions and Configuration section above. Credits These data were produced and analyzed by a collaboration between the Tenenbaum lab at the University at Albany-SUNY, College of Nanoscale Science and Engineering, the Luiz Penalva group at the Greehey Children's Cancer Research Institute, University of Texas Health Science Center and the Microarray Core Facility at the Center for Functional Genomics, Rensselaer, NY . Contact: Scott Tenenbaum References Baroni TE, Chittur SV, George AD, Tenenbaum SA. Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol Biol. 2008;419:93-108. George AD, Tenenbaum SA. MicroRNA modulation of RNA-binding protein regulatory elements. RNA Biol. 2006;3(2):57-9. Epub 2006 Apr 1. Jain R, Devine T, George AD, Chittur SV, Baroni TE, Penalva LO, Tenenbaum SA. RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63 Jayaseelan S, Doyle F, Currenti S, Tenenbaum SA. RIP: An mRNA Localization Technique. Methods Mol Biol. 2011;714:407-422. Keene JD, Tenenbaum SA. Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell. 2002;9(6):1161-7. Penalva LO, Tenenbaum SA, Keene JD. Gene expression analysis of messenger RNP complexes. Methods Mol Biol. 2004;257:125-34. Tenenbaum SA, Carson CC, Lager PJ, Keene JD. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14085-90. Tenenbaum SA, Lager PJ, Carson CC, Keene JD. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods. 2002 Feb;26(2):191-8. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeRbpSuper ENC RNA Binding ENCODE RNA Binding Proteins Regulation Description In eukaryotic organisms, gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs (mRNAs) have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins (RBPs) play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks can elucidate RNA processing by identifying RNA molecules that interact with specific RBPs. They were developed using assays that first purify mRNA-RBP complexes and then separate the complexes to identify the target mRNAs bound to specific RBPs. The mRNAs can be identified by methods including sequencing, microarrays, and SAGE. The tracks in this supertrack contain two forms of information: genes whose transcripts were bound by the given RBP (such as SUNY RIP GeneSt) and approximate location of the RBP binding site in the mRNA sequence (such SUNY RIP Tiling and SUNY RIP-seq). Please note: RIP input tracks (both array and sequencing based) were created for use in downstream informatic analysis to produce RBP specific RIP tracks. Low abundance RNA that is undetectable in the input samples may be proportionally enriched to the point of detection in the RIPs. This may be confusing to some users expecting to see RIP as a subset of input. Users seeking information on total RNA should examine the "expression" RNA-seq tracks produced by other ENCODE groups. Display Conventions and Configuration These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Baroni TE, Chittur SV, George AD, Tenenbaum SA. Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol Biol. 2008;419:93-108. George AD, Tenenbaum SA. MicroRNA modulation of RNA-binding protein regulatory elements. RNA Biol. 2006 Apr;3(2):57-9. Keene JD, Tenenbaum SA. Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell. 2002 Jun;9(6):1161-7. Penalva LO, Tenenbaum SA, Keene JD. Gene expression analysis of messenger RNP complexes. Methods Mol Biol. 2004;257:125-34. Tenenbaum SA, Lager PJ, Carson CC, Keene JD. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods. 2002 Feb;26(2):191-8. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeSunyAlbanyGeneStHepg2RipinputRbpAssocRnaV2 HepG2 RIP-Input ripInput HepG2 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001221 1221 GSM787611 Tenenbaum SunyAlbany Input hg18 wgEncodeSunyAlbanyGeneStHepg2RipinputRbpAssocRnaV2 RbpAssocRna hepatocellular carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HepG2 RIP-Input RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHepg2T7tagRbpAssocRnaV2 HepG2 T7Tag T7Tag HepG2 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001232 1232 GSM787608 Tenenbaum SunyAlbany Nov_69522,Mil_AB3790 antibodies hg18 wgEncodeSunyAlbanyGeneStHepg2T7tagRbpAssocRnaV2 RbpAssocRna T7 (MASMTGGQQMG) hepatocellular carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HepG2 T7Tag RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHepg2Pabpc1RbpAssocRnaV2 HepG2 PABPC1 PABPC1 HepG2 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001231 1231 GSM787617 Tenenbaum SunyAlbany Sig_P6246 antibody hg18 wgEncodeSunyAlbanyGeneStHepg2Pabpc1RbpAssocRnaV2 RbpAssocRna Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). hepatocellular carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HepG2 PABPC1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHepg2Elavl1RbpAssocRnaV2 HepG2 ELAVL1 ELAVL1 HepG2 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001230 1230 GSM787614 Tenenbaum SunyAlbany SC_5261 antibody hg18 wgEncodeSunyAlbanyGeneStHepg2Elavl1RbpAssocRnaV2 RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) hepatocellular carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HepG2 ELAVL1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHelas3RipinputRbpAssocRnaV2 HeLa-S3 RIP-Input ripInput HeLa-S3 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001220 1220 GSM787599 Tenenbaum SunyAlbany Input hg18 wgEncodeSunyAlbanyGeneStHelas3RipinputRbpAssocRnaV2 RbpAssocRna cervical carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HeLa-S3 RIP-Input RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHelas3T7tagRbpAssocRnaV2 HeLa-S3 T7Tag T7Tag HeLa-S3 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001229 1229 GSM787596 Tenenbaum SunyAlbany Nov_69522,Mil_AB3790 antibodies hg18 wgEncodeSunyAlbanyGeneStHelas3T7tagRbpAssocRnaV2 RbpAssocRna T7 (MASMTGGQQMG) cervical carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HeLa-S3 T7Tag RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHelas3Pabpc1RbpAssocRnaV2 HeLa-S3  PABPC1 PABPC1 HeLa-S3 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001228 1228 GSM787605 Tenenbaum SunyAlbany Sig_P6246 antibody hg18 wgEncodeSunyAlbanyGeneStHelas3Pabpc1RbpAssocRnaV2 RbpAssocRna Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). cervical carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HeLa-S3 PABPC1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStHelas3Elavl1RbpAssocRnaV2 HeLa-S3 ELAV1 ELAVL1 HeLa-S3 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001227 1227 GSM787602 Tenenbaum SunyAlbany SC_5261 antibody hg18 wgEncodeSunyAlbanyGeneStHelas3Elavl1RbpAssocRnaV2 RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) cervical carcinoma RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA HeLa-S3 ELAV1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStK562RipinputRbpAssocRnaV2 K562 RIP-Input ripInput K562 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001226 1226 GSM787561 Tenenbaum SunyAlbany Input hg18 wgEncodeSunyAlbanyGeneStK562RipinputRbpAssocRnaV2 RbpAssocRna leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 RIP-Input RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStK562T7tagRbpAssocRnaV2 K562 T7Tag T7Tag K562 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001225 1225 GSM787558 Tenenbaum SunyAlbany Nov_69522 antibody hg18 wgEncodeSunyAlbanyGeneStK562T7tagRbpAssocRnaV2 RbpAssocRna T7 (MASMTGGQQMG) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 T7Tag RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStK562SlbpRbpAssocRnaV2 K562 SLBP SLBP K562 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001224 1224 GSM787573 Tenenbaum SunyAlbany SC_26522,Mil_061376 antibodies hg18 wgEncodeSunyAlbanyGeneStK562SlbpRbpAssocRnaV2 RbpAssocRna Stem-loop binding protein (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 SLBP RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStK562Pabpc1RbpAssocRnaV2 K562 PABPC1 PABPC1 K562 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001223 1223 GSM787567 Tenenbaum SunyAlbany Sig_P6246  antibody hg18 wgEncodeSunyAlbanyGeneStK562Pabpc1RbpAssocRnaV2 RbpAssocRna Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 PABPC1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStK562Elavl1RbpAssocRnaV2 K562 ELAVL1 ELAVL1 K562 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001222 1222 GSM787564 Tenenbaum SunyAlbany SC_5261 antibody hg18 wgEncodeSunyAlbanyGeneStK562Elavl1RbpAssocRnaV2 RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 ELAVL1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStK562Celf1RbpAssocRnaV2 K562 CELF1 CELF1 K562 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-18 2011-03-18 wgEncodeEH001233 1233 GSM787570 Tenenbaum SunyAlbany Mil_05621 antibody hg18 wgEncodeSunyAlbanyGeneStK562Celf1RbpAssocRnaV2 RbpAssocRna Embryo deadenylation element-binding protein homolog (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 CELF1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStH1hescRipinputRbpAssocRnaV2 H1hESC RIP-Input ripInput H1-hESC RipGeneSt ENCODE Mar 2012 Freeze 2010-12-10 2011-09-10 wgEncodeEH001236 1236 GSM787623 Tenenbaum SunyAlbany Input hg18 wgEncodeSunyAlbanyGeneStH1hescRipinputRbpAssocRnaV2 RbpAssocRna embryonic stem cells RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA H1-hESC RIP-Input RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStH1hescT7tagRbpAssocRnaV2 H1hESC T7Tag T7Tag H1-hESC RipGeneSt ENCODE Mar 2012 Freeze 2010-12-10 2011-09-10 wgEncodeEH001235 1235 GSM787620 Tenenbaum SunyAlbany Nov_69522,Mil_AB3790 antibodies hg18 wgEncodeSunyAlbanyGeneStH1hescT7tagRbpAssocRnaV2 RbpAssocRna T7 (MASMTGGQQMG) embryonic stem cells RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA H1-hESC T7Tag RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStH1hescElavl1RbpAssocRnaV2 H1hESC ELAVL1 ELAVL1 H1-hESC RipGeneSt ENCODE Mar 2012 Freeze 2010-12-10 2011-09-10 wgEncodeEH001234 1234 GSM787626 Tenenbaum SunyAlbany SC_5261 antibody hg18 wgEncodeSunyAlbanyGeneStH1hescElavl1RbpAssocRnaV2 RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) embryonic stem cells RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA H1-hESC ELAV1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878RipinputRbpAssocRnaV2 GM12878 RIP-Input ripInput GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001219 1219 GSM787540 Tenenbaum SunyAlbany Input hg18 wgEncodeSunyAlbanyGeneStGm12878RipinputRbpAssocRnaV2 RbpAssocRna B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 RIP-Input RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878T7tagRbpAssocRnaV2 GM12878 T7Tag T7Tag GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001218 1218 GSM787537 Tenenbaum SunyAlbany Nov_69522 antibody hg18 wgEncodeSunyAlbanyGeneStGm12878T7tagRbpAssocRnaV2 RbpAssocRna T7 (MASMTGGQQMG) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 T7Tag RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878SlbpRbpAssocRnaV2 GM12878 SLBP SLBP GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001217 1217 GSM787552 Tenenbaum SunyAlbany SC_26522 antibody hg18 wgEncodeSunyAlbanyGeneStGm12878SlbpRbpAssocRnaV2 RbpAssocRna Stem-loop binding protein (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 SLBP RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878Pabpc1RbpAssocRnaV2 GM12878 PABPC1 PABPC1 GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001216 1216 GSM787546 Tenenbaum SunyAlbany Sig_P6246 antibody hg18 wgEncodeSunyAlbanyGeneStGm12878Pabpc1RbpAssocRnaV2 RbpAssocRna Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 PABPC1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878Igf2bp1RbpAssocRnaV2 GM12878 IGF2BP1 IGF2BP1 GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001215 1215 GSM787555 Tenenbaum SunyAlbany SC_21027 antibody hg18 wgEncodeSunyAlbanyGeneStGm12878Igf2bp1RbpAssocRnaV2 RbpAssocRna Insulin-like growth factor 2 mRNA binding protein 1 (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 IGF2BP1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878Elavl1RbpAssocRnaV2 GM12878 ELAVL1 ELAVL1 GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001214 1214 GSM787543 Tenenbaum SunyAlbany SC_5261 antibody hg18 wgEncodeSunyAlbanyGeneStGm12878Elavl1RbpAssocRnaV2 RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 ELAVL1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyGeneStGm12878Celf1RbpAssocRnaV2 GM12878 CELF1 CELF1 GM12878 RipGeneSt ENCODE Mar 2012 Freeze 2010-06-01 2011-03-01 wgEncodeEH001213 1213 GSM787549 Tenenbaum SunyAlbany Mil_05621 antibody hg18 wgEncodeSunyAlbanyGeneStGm12878Celf1RbpAssocRnaV2 RbpAssocRna Embryo deadenylation element-binding protein homolog (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Gene Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 CELF1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTiling SUNY RIP Tiling GSE40691 RNA Binding Protein Associated RNA by Tiling Array from ENCODE/SUNY Albany Regulation Description This track is produced as part of the ENCODE Project. This track displays transcriptional fragments associated with RNA binding proteins in different cell lines, using RIP-Chip (Ribonomic) profiling on Affymetrix GeneChip ENCODE 2.0R Tiling Arrays. The RBP Assoc RNA view shows the genomic location of transcripts associated with the array probes. Data for this track was produced as part of the Encyclopedia of DNA Elements (ENCODE) Project. In eukaryotic organisms, gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show the associated mRNAs that co-precipitate with the targeted RNA-binding proteins using RIP-Chip profiling. Display Conventions and Configuration This track is a multi-view composite track. For each view there are multiple subtracks that display individually in the browser. The subtracks within this track correspond to different antibodies/target proteins tested in different cell lines. This track is initially released with a single view: RBP Assoc RNA The RBP Assoc RNA view shows the genomic extent of the transcriptional segments associated with the Affymetrix Tiling Array probes. Instructions for configuring multi-view tracks are here. Methods RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols . The associated transcriptional fragments were identified using Affymetrix GeneChip ENCODE 2.0R Tiling Arrays. Arrays were analyzed using Affymetrix Tiling Analysis Software (TAS) version 1.1. Total Input and T7Tag (negative control) tracks were each developed by single sample analysis of their respective triplicate sets with quantile normalization and linear scaling applied. Probe signals were calculated using the Hodges-Lehmann estimator with a bandwidth of 100 bases. Resulting signal files were examined to develop percentiles. Interval analysis was performed using a minimum cut-off equal to the 95th percentile signal score, a minimum run of 21 (3 * platform resolution) and max gap of 63 (9 * platform resolution). Treatment RIP tracks (e.g., ELAVL1, PABC1) were developed by two sample analysis with T7Tag used as the control. Quantile normalization and scaling was applied to these sample groups individually. Probe signals were calculated with the Hodges-Lehmann estimator using signal log (log2) ratios and a bandwidth of 100 bases. Resulting signal files were examined to develop percentiles. Interval analysis was performed using a minimum cut-off equal to the 95th percentile signal ratio score, a minimum run of 21 (3 * platform resolution) and max gap of 63 (9 * platform resolution). For additional RIP methods detail, see Tenenbaum et al. 2002; Baroni et al. 2008; Penalva et al. 2004, below. Verification All experiments (including controls) performed in and analyzed as triplicates. Credits These data were produced and analyzed by a collaboration between the Tenenbaum lab at the University at Albany-SUNY, College of Nanoscale Science and Engineering, the Luiz Penalva group at the Greehey Children's Cancer Research Institute, University of Texas Health Science Center and the Microarray Core Facility at the Center for Functional Genomics, Rensselaer, NY . Contact: &#83;&#84;&#101;&#110;&#101;&#110;&#98;&#97;um&#64;&#117;&#97;m&#97;&#105;&#108;. &#97;&#108;&#98;&#97;ny. &#101;&#100;&#117; References Tenenbaum SA, Lager PJ, Carson CC, Keene JD. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods. 2002 Feb;26(2):191-8. Baroni TE, Chittur SV, George AD, Tenenbaum SA. Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol Biol. 2008;419:93-108. Penalva LO, Tenenbaum SA, Keene JD. Gene expression analysis of messenger RNP complexes. Methods Mol Biol. 2004;257:125-34. Keene JD, Tenenbaum SA. Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell. 2002;9(6):1161-7. George AD, Tenenbaum SA. MicroRNA modulation of RNA-binding protein regulatory elements. RNA Biol. 2006;3(2):57-9. Epub 2006 Apr 1. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeSunyAlbanyTilingView SunyAlbanyTiling RNA Binding Protein Associated RNA by Tiling Array from ENCODE/SUNY Albany Regulation 
wgEncodeSunyAlbanyTilingK562RipinputRbpAssocRna K562 Input ripInput K562 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001261 1261 GSM999236 Tenenbaum SunyAlbany Input wgEncodeSunyAlbanyTilingK562RipinputRbpAssocRna RbpAssocRna leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 Input RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingK562T7tagRbpAssocRna K562 T7Tag T7Tag K562 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001260 1260 GSM999237 Tenenbaum SunyAlbany Nov_69522,Mil_AB3790 antibodies wgEncodeSunyAlbanyTilingK562T7tagRbpAssocRna RbpAssocRna T7 (MASMTGGQQMG) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 T7Tag RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingK562Pabpc1RbpAssocRna K562 PABPC1 PABPC1 K562 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001259 1259 GSM999239 Tenenbaum SunyAlbany Sig_P6246 antibody wgEncodeSunyAlbanyTilingK562Pabpc1RbpAssocRna RbpAssocRna Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 PABPC1 RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingK562Elavl1RbpAssocRna K562 ELAVL1 ELAVL1 K562 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001258 1258 GSM999238 Tenenbaum SunyAlbany SC_5261 antibody wgEncodeSunyAlbanyTilingK562Elavl1RbpAssocRna RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA K562 ELAVL1 RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingGm12878RipinputRbpAssocRna GM12878 Input ripInput GM12878 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001257 1257 GSM999240 Tenenbaum SunyAlbany Input wgEncodeSunyAlbanyTilingGm12878RipinputRbpAssocRna RbpAssocRna B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 Input RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingGm12878T7tagRbpAssocRna GM12878 T7Tag T7Tag GM12878 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001256 1256 GSM999241 Tenenbaum SunyAlbany Nov_69522 antibody wgEncodeSunyAlbanyTilingGm12878T7tagRbpAssocRna RbpAssocRna T7 (MASMTGGQQMG) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 T7Tag RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingGm12878Pabpc1RbpAssocRna GM12878 PABPC1 PABPC1 GM12878 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001255 1255 GSM999243 Tenenbaum SunyAlbany Sig_P6246 antibody wgEncodeSunyAlbanyTilingGm12878Pabpc1RbpAssocRna RbpAssocRna Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 PABPC1 RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyAlbanyTilingGm12878Elavl1RbpAssocRna GM12878 ELAVL1 ELAVL1 GM12878 RipTiling ENCODE June 2010 Freeze 2010-06-01 2011-03-01 wgEncodeEH001254 1254 GSM999242 Tenenbaum SunyAlbany SC_5261 antibody wgEncodeSunyAlbanyTilingGm12878Elavl1RbpAssocRna RbpAssocRna (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Tiling Array Tenenbaum Tenenbaum - SUNY at Albany Ribosome binding protein associated RNA GM12878 ELAVL1 RBP Associated RNA by Tiling Array from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeq SUNY RIP-seq GSE35585 RIP-seq from ENCODE/SUNY Albany Regulation Description The RNA binding protein (RBP) associated mRNA sequencing track (RIP-Seq) is produced as part of the Encyclopedia of DNA Elements (ENCODE) Project. This track displays transcriptional fragments associated with RBP in cell lines K562 and GM12878, using Ribonomic profiling via Illumina SBS. In eukaryotic organisms gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show the associated mRNAs that co-precipitate with the targeted RNA-binding proteins using RIP-Seq profiling. Display Conventions and Configuration This track is a multi-view composite track. For each view there are multiple subtracks that display individually in the browser. The subtracks within this track correspond to different antibodies/target proteins tested in different cell lines. Peaks The Peaks view shows the genomic extent of the sequencing read peaks. Signal Density graph of signal enrichment based on a normalized aligned read density (Read Per Million, RPM). RPM is reported in the score field and is equal to the number of reads at that position divided by the total number of reads divided by one million. The Signal view is unflitered and displays dense, continuous data as a graph and the RPM measure assists in visualizing the relative amount of a given transcript across multiple samples. Alignments The Alignments view shows reads mapped to the genome. The alignment file follows the standard SAM format of Bowtie output. See the Bowtie Manual for more information about the SAM Bowtie output and the SAM Format Specification for more information on the SAM/BAM file format. Instructions for configuring multi-view tracks are here. Methods RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols . RNA samples were amplified and converted to cDNA with the Nugen Ovation&#169; RNA-Seq System and prepped for sequencing with the Illumina mRNA-Seq protocol. Approximately 30 million single end sequencing reads were obtained for each K562 and GM12878. RIP samples were analyzed for signal that was at or above the 60th percentile and statistically enriched compared to the negative control. Sequences were analyzed using TopHat (Trapnell et al., 2009) with Bowtie (Langmead et al., 2009). Peaks were called from the top 40&#37; of TopHat normalized reads, with a max gap, min run of (24:48). Unions of overlapping peak regions from total RNA replicates (RIP-Input) are presented with p-value from a one tailed t-test for average signal from replicates versus 0 (no cut-off was used for totals). Replicate overlap for positive RIP treatment peaks (ELAVL1 and PABPC1) are presented with a p-value from one tailed t-test versus signal for same the region in negative control replicates (T7-tag). RIP peaks were from sequences longer than 120 bp and p-value &lt; .05. For both totals (RIP-input) and RIPs, the peak scores are scaled relative p-values between treatment and control. Credits These data were produced and analyzed by a collaboration between the Tenenbaum lab at the University at Albany-SUNY, College of Nanoscale Science and Engineering,the Luiz Penalva group at the Greehey Children's Cancer Research Institute, University of Texas Health Science Center and the Microarray Core Facility at the Center for Functional Genomics, Rensselaer, NY. Contact: Scott Tenenbaum References Baroni TE, Chittur SV, George AD, Tenenbaum SA. Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling . Methods Mol Biol. 2008;419:93-108. George AD, Tenenbaum SA. MicroRNA modulation of RNA-binding protein regulatory elements . RNA Biol. 2006;3(2):57-9. Epub 2006 Apr 1. Keene JD, Tenenbaum SA. Eukaryotic mRNPs may represent posttranscriptional operons . Mol Cell. 2002;9(6):1161-7. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome . Genome Biology. 2009 Mar; 10:R25. Penalva LO, Tenenbaum SA, Keene JD. Gene expression analysis of messenger RNP complexes . Methods Mol Biol. 2004;257:125-34. Tenenbaum SA, Lager PJ, Carson CC, Keene JD. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays . Methods. 2002 Feb;26(2):191-8. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeSunyRipSeqViewSignal Signal RIP-seq from ENCODE/SUNY Albany Regulation 
wgEncodeSunyRipSeqK562RipinputSigRep2 K562 Input 2 ripInput K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000795 795 GSM944521 Tenenbaum SunyAlbany 2 wgEncodeSunyRipSeqK562RipinputSigRep2 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 RIP-Input RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562RipinputSigRep1 K562 Input 1 ripInput K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000795 795 GSM944521 Tenenbaum SunyAlbany 1 wgEncodeSunyRipSeqK562RipinputSigRep1 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 RIP-Input RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562T7tagSigRep2 K562 T7Tag 2 T7Tag K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000800 800 GSM944526 Tenenbaum SunyAlbany Nov_69522 antibody 2 wgEncodeSunyRipSeqK562T7tagSigRep2 Signal T7 (MASMTGGQQMG) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 T7Tag RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562T7tagSigRep1 K562 T7Tag 1 T7Tag K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000800 800 GSM944526 Tenenbaum SunyAlbany Nov_69522 antibody 1 wgEncodeSunyRipSeqK562T7tagSigRep1 Signal T7 (MASMTGGQQMG) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 T7Tag RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Pabpc1SigRep2 K562 PABPC1 2 PABPC1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000794 794 GSM944522 Tenenbaum SunyAlbany Sig_P6246 antibody 2 wgEncodeSunyRipSeqK562Pabpc1SigRep2 Signal Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 PABPC1 RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Pabpc1SigRep1 K562 PABPC1 1 PABPC1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000794 794 GSM944522 Tenenbaum SunyAlbany Sig_P6246 antibody 1 wgEncodeSunyRipSeqK562Pabpc1SigRep1 Signal Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 PABPC1 RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Elavl1SigRep2 K562 ELAVL1 2 ELAVL1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000793 793 GSM944523 Tenenbaum SunyAlbany SC_5261 antibody 2 wgEncodeSunyRipSeqK562Elavl1SigRep2 Signal (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 ELAVL1 RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Elavl1SigRep1 K562 ELAVL1 1 ELAVL1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000793 793 GSM944523 Tenenbaum SunyAlbany SC_5261 antibody 1 wgEncodeSunyRipSeqK562Elavl1SigRep1 Signal (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal K562 ELAVL1 RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878RipinputSigRep2 GM12878 Input 2 ripInput GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000798 798 GSM944525 Tenenbaum SunyAlbany 2 wgEncodeSunyRipSeqGm12878RipinputSigRep2 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 RIP-Input RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878RipinputSigRep1 GM12878 Input 1 ripInput GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000798 798 GSM944525 Tenenbaum SunyAlbany 1 wgEncodeSunyRipSeqGm12878RipinputSigRep1 Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 RIP-Input RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878T7tagSigRep2 GM12878 T7Tag 2 T7Tag GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000799 799 GSM944524 Tenenbaum SunyAlbany Nov_69522 antibody 2 wgEncodeSunyRipSeqGm12878T7tagSigRep2 Signal T7 (MASMTGGQQMG) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 T7Tag RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878T7tagSigRep1 GM12878 T7Tag 1 T7Tag GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000799 799 GSM944524 Tenenbaum SunyAlbany Nov_69522 antibody 1 wgEncodeSunyRipSeqGm12878T7tagSigRep1 Signal T7 (MASMTGGQQMG) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 T7Tag RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Pabpc1SigRep2 GM12878 PABPC1 2 PABPC1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000797 797 GSM944519 Tenenbaum SunyAlbany Sig_P6246 antibody 2 wgEncodeSunyRipSeqGm12878Pabpc1SigRep2 Signal Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 PABPC1 RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Pabpc1SigRep1 GM12878 PABPC1 1 PABPC1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000797 797 GSM944519 Tenenbaum SunyAlbany Sig_P6246 antibody 1 wgEncodeSunyRipSeqGm12878Pabpc1SigRep1 Signal Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 PABPC1 RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Elavl1SigRep2 GM12878 ELAVL1 2 ELAVL1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000796 796 GSM944520 Tenenbaum SunyAlbany SC_5261 antibody 2 wgEncodeSunyRipSeqGm12878Elavl1SigRep2 Signal (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 ELAVL1 RIP-seq Signal Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Elavl1SigRep1 GM12878 ELAVL1 1 ELAVL1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000796 796 GSM944520 Tenenbaum SunyAlbany SC_5261 antibody 1 wgEncodeSunyRipSeqGm12878Elavl1SigRep1 Signal (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Signal GM12878 ELAVL1 RIP-seq Signal Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqViewPeaks Peaks RIP-seq from ENCODE/SUNY Albany Regulation 
wgEncodeSunyRipSeqK562RipinputPk K562 Input Pk ripInput K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000795 795 GSM944521 Tenenbaum SunyAlbany wgEncodeSunyRipSeqK562RipinputPk Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Regions of enriched signal in experiment K562 RIP-Input RIP-seq Analysis from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Pabpc1Pk K562 PABPC1 Pk PABPC1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000794 794 GSM944522 Tenenbaum SunyAlbany Sig_P6246 antibody wgEncodeSunyRipSeqK562Pabpc1Pk Peaks Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Regions of enriched signal in experiment K562 PABPC1 RIP-seq Analysis from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Elavl1Pk K562 ELAVL1 Pk ELAVL1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH000793 793 GSM944523 Tenenbaum SunyAlbany SC_5261 antibody wgEncodeSunyRipSeqK562Elavl1Pk Peaks (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Regions of enriched signal in experiment K562 ELAVL1 RIP-seq Analysis from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878RipinputPk GM12878 Input Pk ripInput GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH000798 798 GSM944525 Tenenbaum SunyAlbany wgEncodeSunyRipSeqGm12878RipinputPk Peaks B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Regions of enriched signal in experiment GM12878 RIP-Input RIP-seq Analysis from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Pabpc1Pk GM12878 PABPC1 Pk PABPC1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH000797 797 GSM944519 Tenenbaum SunyAlbany Sig_P6246 antibody wgEncodeSunyRipSeqGm12878Pabpc1Pk Peaks Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Regions of enriched signal in experiment GM12878 PABPC1 RIP-seq Analysis from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Elavl1Pk GM12878 ELAVL1 Pk ELAVL1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH000796 796 GSM944520 Tenenbaum SunyAlbany SC_5261 antibody wgEncodeSunyRipSeqGm12878Elavl1Pk Peaks (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Regions of enriched signal in experiment GM12878 ELAVL1 RIP-seq Analysis from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqViewAlignments Alignments RIP-seq from ENCODE/SUNY Albany Regulation 
wgEncodeSunyRipSeqK562RipinputAlnRep2 K562 Input 2 ripInput K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000795 795 Tenenbaum SunyAlbany 2 wgEncodeSunyRipSeqK562RipinputAlnRep2 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 RIP-Input RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562RipinputAlnRep1 K562 Input 1 ripInput K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000795 795 Tenenbaum SunyAlbany 1 wgEncodeSunyRipSeqK562RipinputAlnRep1 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 RIP-Input RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562T7tagAlnRep2 K562 T7Tag 2 T7Tag K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000800 800 Tenenbaum SunyAlbany Nov_69522 antibody 2 wgEncodeSunyRipSeqK562T7tagAlnRep2 Alignments T7 (MASMTGGQQMG) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 T7Tag RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562T7tagAlnRep1 K562 T7Tag 1 T7Tag K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000800 800 Tenenbaum SunyAlbany Nov_69522 antibody 1 wgEncodeSunyRipSeqK562T7tagAlnRep1 Alignments T7 (MASMTGGQQMG) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 T7Tag RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Pabpc1AlnRep2 K562 PABPC1 2 PABPC1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000794 794 Tenenbaum SunyAlbany Sig_P6246 antibody 2 wgEncodeSunyRipSeqK562Pabpc1AlnRep2 Alignments Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 PABPC1 RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Pabpc1AlnRep1 K562 PABPC1 1 PABPC1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000794 794 Tenenbaum SunyAlbany Sig_P6246 antibody 1 wgEncodeSunyRipSeqK562Pabpc1AlnRep1 Alignments Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 PABPC1 RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Elavl1AlnRep2 K562 ELAVL1 2 ELAVL1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000793 793 Tenenbaum SunyAlbany SC_5261 antibody 2 wgEncodeSunyRipSeqK562Elavl1AlnRep2 Alignments (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 ELAVL1 RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqK562Elavl1AlnRep1 K562 ELAVL1 1 ELAVL1 K562 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000793 793 Tenenbaum SunyAlbany SC_5261 antibody 1 wgEncodeSunyRipSeqK562Elavl1AlnRep1 Alignments (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch K562 ELAVL1 RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878RipinputAlnRep2 GM12878 Input 2 ripInput GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000798 798 Tenenbaum SunyAlbany 2 wgEncodeSunyRipSeqGm12878RipinputAlnRep2 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 RIP-Input RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878RipinputAlnRep1 GM12878 Input 1 ripInput GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000798 798 Tenenbaum SunyAlbany 1 wgEncodeSunyRipSeqGm12878RipinputAlnRep1 Alignments B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 RIP-Input RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878T7tagAlnRep2 GM12878 T7Tag 2 T7Tag GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000799 799 Tenenbaum SunyAlbany Nov_69522 antibody 2 wgEncodeSunyRipSeqGm12878T7tagAlnRep2 Alignments T7 (MASMTGGQQMG) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 T7Tag RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878T7tagAlnRep1 GM12878 T7Tag 1 T7Tag GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000799 799 Tenenbaum SunyAlbany Nov_69522 antibody 1 wgEncodeSunyRipSeqGm12878T7tagAlnRep1 Alignments T7 (MASMTGGQQMG) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 T7Tag RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Pabpc1AlnRep2 GM12878 PABPC1 2 PABPC1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000797 797 Tenenbaum SunyAlbany Sig_P6246 antibody 2 wgEncodeSunyRipSeqGm12878Pabpc1AlnRep2 Alignments Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 PABPC1 RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Pabpc1AlnRep1 GM12878 PABPC1 1 PABPC1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000797 797 Tenenbaum SunyAlbany Sig_P6246 antibody 1 wgEncodeSunyRipSeqGm12878Pabpc1AlnRep1 Alignments Poly(A) binding protein, cytoplasmic 1 (Homo sapiens). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 PABPC1 RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Elavl1AlnRep2 GM12878 ELAVL1 2 ELAVL1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000796 796 Tenenbaum SunyAlbany SC_5261 antibody 2 wgEncodeSunyRipSeqGm12878Elavl1AlnRep2 Alignments (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 ELAVL1 RIP-seq Alignments Rep 2 from ENCODE/SUNY Regulation 
wgEncodeSunyRipSeqGm12878Elavl1AlnRep1 GM12878 ELAVL1 1 ELAVL1 GM12878 RipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH000796 796 Tenenbaum SunyAlbany SC_5261 antibody 1 wgEncodeSunyRipSeqGm12878Elavl1AlnRep1 Alignments (Embryonic lethal, abnormal vision, Drosophila)-like 1 (Huantigen R) (Homo sapiens) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus RNA IP Sequencing Tenenbaum Tenenbaum - SUNY at Albany Shows individual reads mapped to the genome and indicates where bases may mismatch GM12878 ELAVL1 RIP-seq Alignments Rep 1 from ENCODE/SUNY Regulation 
wgEncodeSydhHistone SYDH Histone GSE31755 Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard Regulation Description This track, produced as part of the ENCODE Project, displays maps of histone modifications genome-wide using ChIP-seq in different cell lines. The ChIP-seq method involves first using formaldehyde to cross-link histones and other DNA-associated proteins to genomic DNA within cells. The cross-linked chromatin is subsequently extracted, sheared, and immunoprecipitated using specific antibodies. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments. Chemical modifications (e.g. methylation or acetylation) of the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription factors. Shown for each experiment (defined as a particular antibody and a particular cell type) is a track of enrichment for the specifically modified histone (Signal), along with sites that have the greatest enrichment (Peaks). Also, included for each cell type is the input signal, which represents the control condition where no antibody targeting was performed. In general, the following chemical modifications have associated genetic phenotypes: H3K4me3 and H3K9ac are considered to be marks of active or potentially active promoter regions H3K4me1 and H3K27ac are considered to be marks of active or potentially active enhancer regions\ H3K36me3 and H3K79me2 are considered to be marks of transcriptional elongation H3K27me3 and H3K9me3 are considered to be marks of inactive regions. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. For each cell type, this track contains the following views: Peaks Regions of signal enrichment based on processed data (usually normalized data from pooled replicates). Signal Density graph (wiggle) of signal enrichment based on aligned read density. Peaks and signals displayed in this track are the results of pooled replicate sequence. Alignment files for each replicate are available for download. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Briefly, cells were cross-linked, chromatin was extracted and sonicated using a Bioruptor sonicator (Diagenode) to an average size of 300-500 bp, and individual ChIP assays were performed using antibodies to modified histones. For the K562, MCF-7, HCT-116, NTera-2 (NT2-D1), PANC-1 and PBMC histone ChIP-seq samples, immunoprecipitates were collected using protein G-coupled magnetic beads; a detailed ChIP and library protocol can be found at the Roadmap Epigenome Project. For the U2OS histone ChIP-seq samples, immunoprecipitates were collected using StaphA cells. detailed protocol can be found at the UCD Genome Center. --> Library DNA was quantitated using either a Nanodrop or a BioAnalyzer and sequenced on an Illumina GA2. The sequencing reads were mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length &#126;30 bps) that align uniquely to the human genome. From the mapped tags, a signal map of ChIP DNA fragments (average fragment length &#126; 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome. For each 1 Mb segment of each chromosome, a peak height threshold was determined by requiring a false discovery rate &lt;&#61; 0.05 when comparing the number of peaks above threshold as compared to the number obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value &lt;&#61; 0.05 are considered to be significantly enriched compared to the input DNA control. Release Notes This is Release 3 (June 2012) of this track, which adds 9 new experiments for the MCF-7, HCT-116 and PANC-1 cell lines. Credits These data were generated and analyzed by the labs of Peggy Farnham (USC/Norris Cancer Center; previously at UC Davis) and Michael Snyder at Stanford University. Contact: Peggy Farnham for questions concerning data collection and usage and Philip Cayting for data scoring and submission inquiries. References Blahnik KR, Dou L, Echupare L, Iyengar S, O&#39;Geen H, et al. Characterization of the Contradictory Chromatin Signatures at the 3&#39; Exons of Zinc Finger Genes. PLoS One. 2011;6(2):e17121. O&#39;Geen H, Echipare L, Farnham PJ Using ChIP-seq technology to generate high-resolution profiles of histone modifications. Methods Mol Biol. 2011;791;265-286. O&#39;Geen H, Frietze S, Farnham PJ Using ChIP-seq Technology to Identify Targets of Zinc Finger Transcription Factors. Methods Mol Biol. 2010;649:437-455. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeSydhHistoneViewSignal Signal Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard Regulation 
wgEncodeSydhHistoneU2osInputUcdSig U2OS Input Input U2OS UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2010-06-11 2011-03-11 wgEncodeEH000916 916 GSM788069 Snyder USC PeakSeq1.0 input wgEncodeSydhHistoneU2osInputUcdSig None Signal osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal U2OS Input Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneU2osH3k36me3bUcdSig U2OS H3K36me3 H3K36me3B U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-11-02 2011-02-15 wgEncodeEH000920 920 GSM788076 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneU2osH3k36me3bUcdSig None Signal Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal U2OS H3K36me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneU2osH3k9me3UcdSig U2OS H3K9me3 H3K9me3 U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-08-16 2011-05-16 wgEncodeEH000919 919 GSM788078 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneU2osH3k9me3UcdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal U2OS H3K9me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcInputUcdSig PBMC Input Input PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH001883 1883 GSM788070 Snyder USC PeakSeq1.0 input wgEncodeSydhHistonePbmcInputUcdSig None Signal peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBMC Input Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k27me3bUcdSig PBMC H3K27me3 H3K27me3B PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001746 1746 GSM788073 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k27me3bUcdSig None Signal Histone H3 (tri-methyl K27) marks repressed chromatin regions peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBMC H3K27me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k9me3UcdSig PBMC H3K9me3 H3K9me3 PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001748 1748 GSM788079 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k9me3UcdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBMC H3K9me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k04me3bUcdSig PBMC H3K4me3 H3K4me3B PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH001882 1882 GSM788075 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k04me3bUcdSig None Signal Histone H3 (tri-methyl K4) marks promoters in chromatin regions peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBMC H3K4me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k4me1UcdSig PBMC H3K4me1 H3K4me1 PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001747 1747 GSM788084 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k4me1UcdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBMC H3K4me1 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1InputUcdSig PANC-1 Input Input PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002070 2070 GSM818828 Snyder USC PeakSeq1.0 input wgEncodeSydhHistonePanc1InputUcdSig None Signal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PANC-1 Input Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1H3k27acUcdSig PANC-1 H3K27ac H3K27ac PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002080 2080 GSM818826 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePanc1H3k27acUcdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PANC-1 H3K27ac Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1H3k04me3bUcdSig PANC-1 H3K4me3 H3K4me3B PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002876 2876 GSM945856 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePanc1H3k04me3bUcdSig None Signal Histone H3 (tri-methyl K4) marks promoters in chromatin regions pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PANC-1 H3K4me3 Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1H3k04me1bUcdSig PANC-1 H3K4me1 H3K4me1_(pAb-037-050) PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002081 2081 GSM818827 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePanc1H3k04me1bUcdSig None Signal Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution.Histone tails undergo numerous posttranslational modifications. This antibodies recognizes histone H3 monomethylated on lysine 4. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PANC-1 H3K4me1 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1InputUcdSig NT2-D1 Input Input NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000654 654 GSM788077 Snyder USC PeakSeq1.0 input wgEncodeSydhHistoneNt2d1InputUcdSig None Signal malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 Input Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k36me3bUcdSig NT2-D1 H3K36me3 H3K36me3B NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000915 915 GSM788081 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k36me3bUcdSig None Signal Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 H3K36me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k27me3bUcdSig NT2-D1 H3K27me3 H3K27me3B NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000908 908 GSM788071 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k27me3bUcdSig None Signal Histone H3 (tri-methyl K27) marks repressed chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 H3K27me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k9acbUcdSig NT2-D1 H3K9ac H3K9acB NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000910 910 GSM788086 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k9acbUcdSig None Signal Histone H3 (acetyl K9) marks promoters in chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 H3K9ac Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k09me3UcdSig NT2-D1 H3K9me3 H3K9me3 NT2-D1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-22 2010-06-22 2011-03-21 wgEncodeEH000918 918 GSM788080 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k09me3UcdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 H3K9me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k4me3bUcdSig NT2-D1 H3K4me3 H3K4me3B NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000909 909 GSM788072 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k4me3bUcdSig None Signal Histone H3 (tri-methyl K4) marks promoters in chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 H3K4me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k4me1UcdSig NT2-D1 H3K4me1 H3K4me1 NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-22 2011-03-21 wgEncodeEH000917 917 GSM788083 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k4me1UcdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2D1 H3K4me1 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneHct116InputUcdSig HCT-116 Input Input HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH000627 627 GSM945855 Snyder USC PeakSeq1.0 input wgEncodeSydhHistoneHct116InputUcdSig None Signal colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HCT-116 Input Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneHct116H3k27acUcdSig HCT-116 H3K27ac H3K27ac HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002873 2873 GSM945853 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneHct116H3k27acUcdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HCT-116 H3K27ac Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneHct116H3k04me1UcdSig HCT-116 H3K4me1 H3K4me1 HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002874 2874 GSM945858 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneHct116H3k04me1UcdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HCT-116 H3K4me1 Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7InputUcdSig MCF7 Inupt Input MCF-7 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000762 762 GSM945859 Snyder USC hg18 input wgEncodeSydhHistoneMcf7InputUcdSig None Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 Input Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k36me3bUcdSig MCF-7 H3K36me3 H3K36me3B MCF-7 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-06-07 2013-03-07 wgEncodeEH002923 2923 GSM970217 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k36me3bUcdSig None Signal Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 H3K36me3 Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k27me3bUcdSig MCF-7 H3K27me3 H3K27me3B MCF-7 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-06-07 2013-03-07 wgEncodeEH002922 2922 GSM970218 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k27me3bUcdSig None Signal Histone H3 (tri-methyl K27) marks repressed chromatin regions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 H3K27me3 Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k27acUcdSig MCF-7 H3K27ac H3K27ac MCF-7 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-01-22 2012-10-21 wgEncodeEH002872 2872 GSM945854 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k27acUcdSig None Signal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 H3K27ac Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k09me3UcdSig MCF-7 H3K9me3 H3K9me3 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002875 2875 GSM945857 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k09me3UcdSig None Signal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 H3K9me3 Histone Modifications by ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562InputUcdSig K562 Input Input K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-03-22 2009-06-11 2010-03-11 wgEncodeEH000672 672 GSM788074 Snyder USC hg18 input wgEncodeSydhHistoneK562InputUcdSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 Input Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k27me3bUcdSig K562 H3K27me3 H3K27me3B K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000912 912 GSM788088 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k27me3bUcdSig None Signal Histone H3 (tri-methyl K27) marks repressed chromatin regions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 H3K27me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k9acbUcdSig K562 H3K9ac H3K9acB K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000914 914 GSM788082 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k9acbUcdSig None Signal Histone H3 (acetyl K9) marks promoters in chromatin regions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 H3K9ac Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k4me3bUcdSig K562 H3K4me3 H3K4me3B K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000913 913 GSM788087 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k4me3bUcdSig None Signal Histone H3 (tri-methyl K4) marks promoters in chromatin regions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 H3K4me3 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k4me1UcdSig K562 H3K4me1 H3K4me1 K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH000911 911 GSM788085 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k4me1UcdSig None Signal Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 H3K4me1 Histone Modifications by ChIP-Seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneViewPeaks Peaks Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard Regulation 
wgEncodeSydhHistoneU2osH3k36me3bUcdPk U2OS H3K36me3 H3K36me3B U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-11-02 2011-02-15 wgEncodeEH000920 920 GSM788076 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneU2osH3k36me3bUcdPk None Peaks Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment U2OS H3K36me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneU2osH3k9me3UcdPk U2OS H3K9me3 H3K9me3 U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-08-16 2011-05-16 wgEncodeEH000919 919 GSM788078 Snyder USC PeakSeq1.0.  Submitted even though replicate peak overlap below threshold because data visually looks good, but calling peaks for H3K9me3 is very difficult due to the nature of the signal and not the quality of the data.  When we call peaks using our program that has been modified for histones, we get a ~60% overlap. That's about as good as it gets with H3K9me3 peak calling. exp wgEncodeSydhHistoneU2osH3k9me3UcdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment U2OS H3K9me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k27me3bUcdPk PBMC H3K27me3 H3K27me3B PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001746 1746 GSM788073 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k27me3bUcdPk None Peaks Histone H3 (tri-methyl K27) marks repressed chromatin regions peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBMC H3K27me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k9me3UcdPk PBMC H3K9me3 H3K9me3 PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001748 1748 GSM788079 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k9me3UcdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBMC H3K9me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k04me3bUcdPk PBMC H3K4me3 H3K4me3B PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEH001882 1882 GSM788075 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k04me3bUcdPk None Peaks Histone H3 (tri-methyl K4) marks promoters in chromatin regions peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBMC H3K4me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePbmcH3k4me1UcdPk PBMC H3K4me1 H3K4me1 PBMC UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001747 1747 GSM788084 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePbmcH3k4me1UcdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. peripheral blood mononuclear cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBMC H3K4me1 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1H3k27acUcdPk PANC-1 H3K27ac H3K27ac PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002080 2080 GSM818826 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePanc1H3k27acUcdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PANC-1 H3K27ac Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1H3k04me3bUcdPk PANC-1 H3K4me3 H3K4me3B PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002876 2876 GSM945856 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePanc1H3k04me3bUcdPk None Peaks Histone H3 (tri-methyl K4) marks promoters in chromatin regions pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PANC-1 H3K4me3 Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistonePanc1H3k04me1bUcdPk PANC-1 H3K4me1 H3K4me1_(pAb-037-050) PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002081 2081 GSM818827 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistonePanc1H3k04me1bUcdPk None Peaks Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution.Histone tails undergo numerous posttranslational modifications. This antibodies recognizes histone H3 monomethylated on lysine 4. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PANC-1 H3K4me1 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k36me3bUcdPk NT2-D1 H3K36me3 H3K36me3B NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000915 915 GSM788081 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k36me3bUcdPk None Peaks Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2D1 H3K36me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k27me3bUcdPk NT2-D1 H3K27me3 H3K27me3B NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000908 908 GSM788071 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k27me3bUcdPk None Peaks Histone H3 (tri-methyl K27) marks repressed chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2D1 H3K27me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k9acbUcdPk NT2-D1 H3K9ac H3K9acB NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000910 910 GSM788086 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k9acbUcdPk None Peaks Histone H3 (acetyl K9) marks promoters in chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2D1 H3K9ac Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k09me3UcdPk NT2-D1 H3K9me3 H3K9me3 NT2-D1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-22 2010-06-22 2011-03-21 wgEncodeEH000918 918 GSM788080 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k09me3UcdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2D1 H3K9me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k4me3bUcdPk NT2-D1 H3K4me3 H3K4me3B NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-04 2011-02-04 wgEncodeEH000909 909 GSM788072 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k4me3bUcdPk None Peaks Histone H3 (tri-methyl K4) marks promoters in chromatin regions malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2D1 H3K4me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneNt2d1H3k4me1UcdPk NT2-D1 H3K4me1 H3K4me1 NT2-D1 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-22 2011-03-21 wgEncodeEH000917 917 GSM788083 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneNt2d1H3k4me1UcdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2D1 H3K4me1 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneHct116H3k27acUcdPk HCT-116 H3K27ac H3K27ac HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002873 2873 GSM945853 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneHct116H3k27acUcdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HCT-116 H3K27ac Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneHct116H3k04me1UcdPk HCT-116 H3K4me1 H3K4me1 HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002874 2874 GSM945858 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneHct116H3k04me1UcdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HCT-116 H3K4me1 Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k36me3bUcdPk MCF-7 H3K36me3 H3K36me3B MCF-7 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-06-07 2013-03-07 wgEncodeEH002923 2923 GSM970217 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k36me3bUcdPk None Peaks Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 H3K36me3 Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k27me3bUcdPk MCF-7 H3K27me3 H3K27me3B MCF-7 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-06-07 2013-03-07 wgEncodeEH002922 2922 GSM970218 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k27me3bUcdPk None Peaks Histone H3 (tri-methyl K27) marks repressed chromatin regions mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 H3K27me3 Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k27acUcdPk MCF-7 H3K27ac H3K27ac MCF-7 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-01-22 2012-10-21 wgEncodeEH002872 2872 GSM945854 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneMcf7H3k27acUcdPk None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 H3K27ac Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneMcf7H3k09me3UcdPk MCF-7 H3K9me3 H3K9me3 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002875 2875 GSM945857 Snyder USC PeakSeq1.0. Spreading mark so standard peak calling does not work well.  Replicates appear to agree regardless. exp wgEncodeSydhHistoneMcf7H3k09me3UcdPk None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 H3K9me3 Histone Modifications by ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k27me3bUcdPk K562 H3K27me3 H3K27me3B K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000912 912 GSM788088 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k27me3bUcdPk None Peaks Histone H3 (tri-methyl K27) marks repressed chromatin regions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 H3K27me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k9acbUcdPk K562 H3K9ac H3K9acB K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000914 914 GSM788082 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k9acbUcdPk None Peaks Histone H3 (acetyl K9) marks promoters in chromatin regions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 H3K9ac Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k4me3bUcdPk K562 H3K4me3 H3K4me3B K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH000913 913 GSM788087 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k4me3bUcdPk None Peaks Histone H3 (tri-methyl K4) marks promoters in chromatin regions leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 H3K4me3 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhHistoneK562H3k4me1UcdPk K562 H3K4me1 H3K4me1 K562 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH000911 911 GSM788085 Snyder USC PeakSeq1.0 exp wgEncodeSydhHistoneK562H3k4me1UcdPk None Peaks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 H3K4me1 Histone Modifications by ChIP-Seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhRnaSeq SYDH RNA-seq GSE35587 RNA-seq from ENCODE/Stanford/Yale/USC/Harvard Expression Description The tracks show enrichment of RNA sequence tags generated by high throughput sequencing (RNA-seq) and mapped to the human genome. Double stranded cDNA was synthesized from polyadenylated RNA (polyA+) . PCR amplified, adapter ligated cDNA, 150-300nt long, was sequenced on an Illumina GA sequencer. Where designated, cell lines received specific treatments prior to RNA isolation. As indicated, K562 cells were treated with either interferon-a or interferon-g for 30 minutes or 6 hours. These experiments were carried out in conjunction with ChIP-Seq experiments on the transcription factors STAT1 and STAT2 in order to examine the effects that inducers of a specific transcriptional response might have on gene expression and on transcription factor binding site discovery. K562 cells were treated with a-amanitin in order to examine the effects of RNA polymerase II inhibition on RNA polymerase III-mediated transcription. This track shows expression data generated as confirmation of the SYDH TFBS tracks.--> SYDH TFBS tracks currently available on genome-preview. Display Conventions and Configuration This is a composite track that contains multiple data types (views). Instructions for configuring composite tracks are here. Raw SignalDensity graph (wiggle) of signal enrichment. Alignments The Alignments view shows reads mapped to the genome and indicates where bases may mismatch. The alignment file follows the standard SAM format of Bowtie output with the following additions: the custom tags X0 X1 XN XM XO XG XT XA XS XF XE are present. These tags are described by the BWA specifications. See the Bowtie Manual for more information about the SAM Bowtie output (including other tags) and the SAM Format Specification for more information on the SAM/BAM file format. Methods Cells were grown according to the approved ENCODE cell culture protocols. Total RNA was extracted using TRIzol reagents (15596-018, Life Tech), following the manufacturer's protocol. For polyA+ samples, polyadenylated RNA was purified using the MicroPoly(A) Purist kit (AM1919, Life Tech) and fragmented using RNA Fragmentation Reagent (AM8740, Life Tech). Illumina adapters were ligated to double stranded cDNA which was synthesized using reagents from Life Tech (11917-010). PCR amplified adapter ligated cDNA (150-300 bp) was sequenced using Illumina GA. Sequence reads of 27-33nt long with 0-2 mismatches were mapped to the genome. The signal height corresponds to the number of overlapping fragments at each nucleotide position in the genome. Samples originally mapped to the hg18 version of the human genome were remapped to hg19 using the BWA aligner, version 0.5.7. Credits These data were generated and analyzed by the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University; Peggy Farnham at USC; and Kevin Struhl at Harvard. &nbsp;&nbsp; Contact: Gerstein Lab. References Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008 Jun 6;320(5881):1344-9. Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, Struhl K, Snyder M. Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3639-44. Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S et al. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5254-9. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeSydhRnaSeqViewSignal Signal RNA-seq from ENCODE/Stanford/Yale/USC/Harvard Expression 
wgEncodeSydhRnaSeqK562Ifng6hPolyaRaw K562 pA+ Ng6h K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH000527 527 GSM922958 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifng6hPolyaRaw IFNg6h RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA Interferon gamma treatment - 6 hours (Snyder) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 polyA+ IFNg6h RNA-seq Raw Signal from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqK562Ifng30PolyaRaw K562 pA+ Ng30 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH000526 526 GSM922957 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifng30PolyaRaw IFNg30 RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA Interferon gamma treatment - 30 minutes (Snyder) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 polyA+ IFNg30 RNA-seq Raw Signal from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqK562Ifna6hPolyaRaw K562 pA+ Na6h K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH000525 525 GSM922956 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifna6hPolyaRaw IFNa6h RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA Interferon alpha treatment - 6 hours (Snyder) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 polyA+ IFNa6h RNA-seq Raw Signal from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqK562Ifna30PolyaRaw K562 pA+ Na30 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-12-17 2011-09-17 wgEncodeEH000524 524 GSM922955 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifna30PolyaRaw IFNa30 RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA 30 m of Interferon alpha (Snyder) Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 polyA+ IFNa30 RNA-seq Raw Signal from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqViewAlignments Alignments RNA-seq from ENCODE/Stanford/Yale/USC/Harvard Expression 
wgEncodeSydhRnaSeqK562Ifng6hPolyaAln K562 pA+ Ng6h K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-23 2010-09-24 2010-06-24 wgEncodeEH000527 527 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifng6hPolyaAln IFNg6h Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA Interferon gamma treatment - 6 hours (Snyder) Shows individual reads mapped to the genome and indicates where bases may mismatch K562 polyA+ IFNg6h RNA-seq Alignments from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqK562Ifng30PolyaAln K562 pA+ Ng30 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-23 2010-09-24 2010-06-24 wgEncodeEH000526 526 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifng30PolyaAln IFNg30 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA Interferon gamma treatment - 30 minutes (Snyder) Shows individual reads mapped to the genome and indicates where bases may mismatch K562 polyA+ IFNg30 RNA-seq Alignments from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqK562Ifna6hPolyaAln K562 pA+ Na6h K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-23 2010-09-24 2010-06-24 wgEncodeEH000525 525 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifna6hPolyaAln IFNa6h Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA Interferon alpha treatment - 6 hours (Snyder) Shows individual reads mapped to the genome and indicates where bases may mismatch K562 polyA+ IFNa6h RNA-seq Alignments from ENCODE/SYDH Expression 
wgEncodeSydhRnaSeqK562Ifna30PolyaAln K562 pA+ Na30 K562 RnaSeq ENCODE Jan 2011 Freeze 2010-07-23 2010-09-24 2010-06-24 wgEncodeEH000524 524 Snyder Yale hg18 polyA wgEncodeSydhRnaSeqK562Ifna30PolyaAln IFNa30 Alignments leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Sequencing analysis of RNA expression Snyder Snyder - Yale University Isolated Poly(A) RNA 30 m of Interferon alpha (Snyder) Shows individual reads mapped to the genome and indicates where bases may mismatch K562 polyA+ IFNa30 RNA-seq Alignments from ENCODE/SYDH Expression 
wgEncodeSydhTfbs SYDH TFBS GSE31477 Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard Regulation Description This track shows probable binding sites of the specified transcription factors (TFs) in the given cell types as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq). Included for each cell type is the input signal, which represents the control condition where no antibody targeting was performed. For each experiment (cell type vs. antibody) this track shows a graph of enrichment for TF binding (Signal), along with sites that have the greatest evidence of transcription factor binding (Peaks). The sequence reads, quality scores, and alignment coordinates from these experiments are available for download. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. ENCODE tracks typically contain one or more of the following views: Peaks Regions of signal enrichment based on processed data (normalized data from pooled replicates). ENCODE Peaks tables contain fields for statistical significance, including the minimum false discovery rate (FDR) threshold at which the test may be called significant (qValue). SignalDensity graph (wiggle) of signal enrichment based on processed data. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Further preparations were similar to those previously published (Euskirchen et al., 2007) with the exceptions that the cells were unstimulated and sodium orthovanadate was omitted from the buffers. For details on the chromatin immunoprecipitation protocol used, see (Euskirchen et al., 2007) and (Rozowsky et al., 2009). DNA recovered from the precipitated chromatin was sequenced on the Illumina (Solexa) sequencing platform and mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length ~30 bp) that align uniquely to the human genome. From the mapped tags a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome. For each 1 Mb segment of each chromosome a peak height threshold was determined by requiring a false discovery rate less than or equal to 0.05 when comparing the number of peaks above threshold as compared the number obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value less than or equal to 0.05 are considered to be significantly enriched compared to the input DNA control. Release Notes This is Release 3 (August 2012). This release adds in 37 new experiments including 1 new cell line and 7 new antibodies. Credits These data were generated and analyzed by the labs of Michael Snyder at Stanford University; Mark Gerstein and Sherman Weissman at Yale University; Peggy Farnham at University of Southern California; and Kevin Struhl at Harvard. Contact: Philip Cayting. References Cao AR, Rabinovich R, Xu M, Xu X, Jin VX, Farnham PJ. Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome. J Biol Chem. 2011 Apr 8;286(14):11985-96. Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M et al. CREB binds to multiple loci on human chromosome 22. Mol Cell Biol. 2004 May;24(9):3804-14. Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 2007 Jun;17(6):898-909. Iyengar S, Ivanov AV, Jin VX, Rauscher FJ 3rd, Farnham PJ. Functional analysis of KAP1 genomic recruitment. Mol Cell Biol. 2011 May;31(9):1833-47. Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M et al. Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12247-52. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007 Aug;4(8):651-7. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 2009 Jan;27(1):66-75. Publications Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH. Autophagy driven by a master regulator of hematopoiesis. Mol Cell Biol. 2012 Jan;32(1):226-39. Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L. SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. Mol Cell. 2011 Nov 4;44(3):410-23. Linnemann AK, O'Geen H, Keles S, Farnham PJ, Bresnick EH. Genetic framework for GATA factor function in vascular biology. Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13641-6. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeSydhTfbsViewSignal Signal Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard Regulation 
wgEncodeSydhTfbsU2osInputUcdSig U2OS Inpt UCD Input U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH000916 916 GSM935288 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsU2osInputUcdSig None Signal osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal U2OS Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsU2osSetdb1UcdSig U2OS STDB UCD SETDB1 U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001762 1762 GSM935458 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsU2osSetdb1UcdSig None Signal SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal U2OS SETDB1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsU2osKap1UcdSig U2OS KAP1 UCD KAP1 U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-05-31 wgEncodeEH001776 1776 GSM935587 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsU2osKap1UcdSig None Signal KRAB Associated Protein 1, helps regulate transcriptional repression. osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal U2OS KAP1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsShsy5yInputUcdSig SHSY Inpt UCD Input SH-SY5Y UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-02-03 2011-11-03 wgEncodeEH001783 1783 GSM935321 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsShsy5yInputUcdSig None Signal neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal SH-SY5Y Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsShsy5yGata3sc269sc269UcdSig SHSY GAT3 UCD GATA3_(SC-269) SH-SY5Y UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002031 2031 GSM935567 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsShsy5yGata3sc269sc269UcdSig None Signal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq) neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal SH-SY5Y GATA3 SC269 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsShsy5yGata2UcdSig SHSY GAT2 UCD GATA-2 SH-SY5Y UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001770 1770 GSM935589 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsShsy5yGata2UcdSig None Signal GATA binding protein 2 neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal SH-SY5Y GATA2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsRajiInputUcdSig Raji Inpt UCD Input Raji UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001760 1760 GSM935460 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsRajiInputUcdSig None Signal B lymphocyte, "The Raji line of lymphoblast-like cells was established by R.J.V. Pulvertaft in 1963 from a Burkitt's lymphoma of the left maxilla of an 11-year-old Black male." - ATCC. (PMID: 14086209) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal Raji Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsRajiPol2UcdSig Raji Pol2 UCD Pol2 Raji UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001761 1761 GSM935461 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsRajiPol2UcdSig None Signal RNA Polymerase II B lymphocyte, "The Raji line of lymphoblast-like cells was established by R.J.V. Pulvertaft in 1963 from a Burkitt's lymphoma of the left maxilla of an 11-year-old Black male." - ATCC. (PMID: 14086209) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal Raji Pol2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdefetalInputUcdSig PBDF Inpt UCD Input PBDEFetal UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001786 1786 GSM935334 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsPbdefetalInputUcdSig None Signal peripheral blood-derived erythroblasts from 16-19 week human fetal liver Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBDE-Fetal Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdefetalGata1UcdSig PBDF GAT1 UCD GATA-1 PBDEFetal UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001785 1785 GSM935333 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPbdefetalGata1UcdSig None Signal GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. peripheral blood-derived erythroblasts from 16-19 week human fetal liver Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBDE-Fetal GATA1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdeInputUcdSig PBDE Inpt UCD Input PBDE UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-14 wgEncodeEH001778 1778 GSM935593 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsPbdeInputUcdSig None Signal peripheral blood-derived erythroblasts Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBDE Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdePol2UcdSig PBDE Pol2 UCD Pol2 PBDE UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-10-13 2011-07-13 wgEncodeEH001766 1766 GSM935462 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPbdePol2UcdSig None Signal RNA Polymerase II peripheral blood-derived erythroblasts Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBDE Pol2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdeGata1UcdSig PBDE GAT1 UCD GATA-1 PBDE UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-09-23 2011-06-23 wgEncodeEH001765 1765 GSM935465 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPbdeGata1UcdSig None Signal GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. peripheral blood-derived erythroblasts Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PBDE GATA1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPanc1InputUcdSig PANC Inpt UCD Input PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002070 2070 GSM935617 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsPanc1InputUcdSig None Signal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PANC1 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPanc1Tcf7l2UcdSig PANC TCF7L2 UCD TCF7L2 PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002071 2071 GSM816437 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPanc1Tcf7l2UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal PANC1 TCF7L2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1InputUcdSig NT2D Inpt UCD Input NT2-D1 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000654 654 GSM935421 Snyder USC hg18 input wgEncodeSydhTfbsNt2d1InputUcdSig None Signal malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2-D1 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1Znf274UcdSig NT2D Z274 UCD ZNF274 NT2-D1 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001775 1775 GSM935584 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsNt2d1Znf274UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2-D1 ZNF274 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1Yy1UcdSig NT2D YY1 UCD YY1 NT2-D1 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000653 653 GSM935424 Snyder USC hg18 exp wgEncodeSydhTfbsNt2d1Yy1UcdSig None Signal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2-D1 YY1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1Suz12UcdSig NT2D SZ12 UCD SUZ12 NT2-D1 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000652 652 GSM935423 Snyder USC hg18 exp wgEncodeSydhTfbsNt2d1Suz12UcdSig None Signal Suppressor of zeste 12 homolog, Polycomb group (PcG) protein, Component of the PRC2/EED-EZH2 complex malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal NT2-D1 SUZ12 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4InputStdSig NB4 Inpt Std Input NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000617 617 GSM935359 Snyder Yale hg18 input wgEncodeSydhTfbsNb4InputStdSig None Signal acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal NB4 Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4Pol2StdSig NB4 Pol2 Std Pol2 NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000618 618 GSM935354 Snyder Yale hg18 exp wgEncodeSydhTfbsNb4Pol2StdSig None Signal RNA Polymerase II acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal NB4 Pol2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4MaxStdSig NB4 Max Std Max NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-26 2011-05-26 wgEncodeEH001806 1806 GSM935644 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsNb4MaxStdSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal NB4 Max Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4CmycStdSig NB4 cMyc Std c-Myc NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-26 2011-05-26 wgEncodeEH001807 1807 GSM935643 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsNb4CmycStdSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal NB4 c-Myc Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesInputStdSig MCF1 Inpt Std Input MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2011-02-03 2011-11-03 wgEncodeEH001782 1782 GSM935641 Snyder Harvard PeakSeq1.0 hg19 input wgEncodeSydhTfbsMcf10aesInputStdSig None Signal mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal MCF10A Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesInputEtoh01cStdSig MCF1 Et12 Inpt Sd Input MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-13 wgEncodeEH001869 1869 GSM935550 Snyder Harvard PeakSeq1.0 hg19 input wgEncodeSydhTfbsMcf10aesInputEtoh01cStdSig EtOH_0.01pct_12hr Signal mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University 12 h with 0.01% Ethanol (Snyder) Signal MCF10A Input Standard EtOH .01% 36h 12h ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesInputEtoh01bStdSig MCF1 Et4h Inpt Sd Input MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-13 wgEncodeEH001870 1870 GSM935418 Snyder Harvard PeakSeq1.0 hg19 input wgEncodeSydhTfbsMcf10aesInputEtoh01bStdSig EtOH_0.01pct_4hr Signal mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University 4 h with 0.01% Ethanol (Snyder) Signal MCF10A Input Standard EtOH .01% 36h 4h ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesInputHvdSig MCF1 Input Hvd Input MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Jul 2012 Freeze 2012-04-25 2013-01-25 wgEncodeEH002871 2871 GSM935605 Snyder Harvard PeakSeq1.0 input wgEncodeSydhTfbsMcf10aesInputHvdSig None Signal mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal MCF10A Input Harvard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesStat3TamStdSig MCF1 TAM STA3 Std STAT3 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001769 1769 GSM935457 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesStat3TamStdSig 4OHTAM_1uM_36hr Signal Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Signal MCF10A STAT3 Standard 4-hydroxytamoxifen 36hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesStat3Etoh01StdSig MCF1 EtH STA3 Std STAT3 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001772 1772 GSM935591 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesStat3Etoh01StdSig EtOH_0.01pct Signal Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Signal MCF10A STAT3 Standard EtOH .01% 36h ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesStat3Tam112hHvdSig MCF1 TAM 12h STA3 STAT3 MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002836 2836 GSM935399 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesStat3Tam112hHvdSig 4OHTAM_1uM_12hr Signal Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Signal MCF10A STAT3 Harvard 4-hydroxytamoxifen 12hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesPol2TamStdSig MCF1 TAM Pol2 Std Pol2 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001768 1768 GSM935456 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesPol2TamStdSig 4OHTAM_1uM_36hr Signal RNA Polymerase II mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Signal MCF10A Pol2 Standard 4-hydroxytamoxifen 36hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesPol2Etoh01StdSig MCF1 EtH Pol2 Std Pol2 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001771 1771 GSM935588 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesPol2Etoh01StdSig EtOH_0.01pct Signal RNA Polymerase II mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Signal MCF10A Pol2 Standard EtOH .01% 36h ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesE2f4TamHvdSig MCF1 TAM E2F4 Hvd E2F4 MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002835 2835 GSM935400 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesE2f4TamHvdSig 4OHTAM_1uM_36hr Signal mapping at the C-terminus of E2F4 of human origin mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Signal MCF10A E2F4 Harvard 4-hydroxytamoxifen 36hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCmycTam14hHvdSig MCF1 TAM 14h cMyc c-Myc MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002840 2840 GSM935491 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCmycTam14hHvdSig 4OHTAM_1uM_4hr Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Signal MCF10A c-Myc Harvard 4-hydroxytamoxifen 14hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCmycEtoh01HvdSig MCF1 EtH cMyc Hvd c-Myc MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002816 2816 GSM935441 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCmycEtoh01HvdSig EtOH_0.01pct Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Signal MCF10A c-Myc Harvard EtOH .01% 36h ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosTam14hHvdSig MCF1 TAM 14h cFOS c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002838 2838 GSM935397 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosTam14hHvdSig 4OHTAM_1uM_4hr Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Signal MCF10A c-FOS Harvard 4-hydroxytamoxifen 14hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosTam112hHvdSig MCF1 TAM 12h cFOS c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002837 2837 GSM935398 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosTam112hHvdSig 4OHTAM_1uM_12hr Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Signal MCF10A c-FOS Harvard 4-hydroxytamoxifen 12hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosTamHvdSig MCF1 TAM cFOS Hvd c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002839 2839 GSM935396 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosTamHvdSig 4OHTAM_1uM_36hr Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Signal MCF10A c-FOS Harvard 4-hydroxytamoxifen 36hr ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosEtoh01HvdSig MCF1 EtH cFOS Hvd c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002815 2815 GSM935438 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosEtoh01HvdSig EtOH_0.01pct Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Signal MCF10A c-FOS Harvard EtOH .01% 36h ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293tInputUcdSig HEKT Inpt UCD Input HEK293-T-REx UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-02-03 2011-11-03 wgEncodeEH001784 1784 GSM935327 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsHek293tInputUcdSig None Signal embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line, hypotriploid, XXX Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEK293-T-REx Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293tZnf263UcdSig HEKT Z263 UCD ZNF263 HEK293-T-REx UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-24 2011-10-24 wgEncodeEH001781 1781 GSM935577 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293tZnf263UcdSig None Signal ZNF263 (NP_005732, 201 a.a. ~ 299 a.a) partial recombinant protein with GST tag. embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line, hypotriploid, XXX Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEK293-T-REx ZNF263 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293InputUcdSig HEK2 Inpt UCD Input HEK293 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-14 2011-10-13 wgEncodeEH001777 1777 GSM935586 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsHek293InputUcdSig None Signal embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEK293 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293InputStdSig HEK2 Inpt Std Input HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000631 631 GSM935533 Snyder Yale hg18 input wgEncodeSydhTfbsHek293InputStdSig None Signal embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HEK293 Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Tcf7l2UcdSig HEK2 TCF7L2 UCD TCF7L2 HEK293 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-22 2012-03-22 wgEncodeEH002022 2022 GSM782124 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293Tcf7l2UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEK293 TCF7L2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Pol2StdSig HEK2 Pol2 Std Pol2 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000632 632 GSM935534 Snyder Yale hg18 exp wgEncodeSydhTfbsHek293Pol2StdSig None Signal RNA Polymerase II embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HEK293 Pol2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Kap1UcdSig HEK2 KAP1 UCD KAP1 HEK293 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-05-31 wgEncodeEH001779 1779 GSM935592 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293Kap1UcdSig None Signal KRAB Associated Protein 1, helps regulate transcriptional repression. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEK293 KAP1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Elk4UcdSig HEK2 ELK4 UCD ELK4 HEK293 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-05-31 wgEncodeEH001773 1773 GSM935590 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293Elk4UcdSig None Signal This gene is a member of the Ets family of transcription factors and of the ternary complex factor (TCF) subfamily. (provided by RefSeq) embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEK293 ELK4 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHct116InputUcdSig HCT Inpt UCD Input HCT-116 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000627 627 GSM817344 Snyder USC hg18 input wgEncodeSydhTfbsHct116InputUcdSig None Signal colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HCT-116 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHct116Tcf7l2UcdSig HCT TCF7L2 UCD TCF7L2 HCT-116 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000629 629 GSM782123 Snyder USC hg18 exp wgEncodeSydhTfbsHct116Tcf7l2UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HCT-116 TCF7L2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHct116Pol2UcdSig HCT Pol2 UCD Pol2 HCT-116 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000651 651 GSM935426 Snyder USC hg18 exp wgEncodeSydhTfbsHct116Pol2UcdSig None Signal RNA Polymerase II colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HCT-116 Pol2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19193InputTnfaIggrabSig GM93 TNF Inpt IgR Input GM19193 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000779 779 GSM935454 Snyder Stanford hg18 input wgEncodeSydhTfbsGm19193InputTnfaIggrabSig TNFa Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM19193 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19193InputIggmusSig GM93 Inpt IgM Input GM19193 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000742 742 GSM935324 Snyder Stanford hg18 input wgEncodeSydhTfbsGm19193InputIggmusSig None Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM19193 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19193Pol2IggmusSig GM93 Pol2 IgM Pol2 GM19193 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000743 743 GSM935325 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19193Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM19193 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19193NfkbTnfaIggrabSig GM93 TNF NKB IgR NFKB GM19193 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000718 718 GSM935279 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19193NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM19193 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19099InputTnfaIggrabSig GM99 TNF Inpt IgR Input GM19099 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000778 778 GSM935455 Snyder Stanford hg18 input wgEncodeSydhTfbsGm19099InputTnfaIggrabSig TNFa Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM19099 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19099InputIggmusSig GM99 Inpt IgM Input GM19099 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000740 740 GSM935322 Snyder Stanford hg18 input wgEncodeSydhTfbsGm19099InputIggmusSig None Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM19099 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19099Pol2IggmusSig GM99 Pol2 IgM Pol2 GM19099 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000741 741 GSM935323 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19099Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM19099 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19099NfkbTnfaIggrabSig GM99 TNF NKB IgR NFKB GM19099 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000717 717 GSM935273 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19099NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM19099 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18951InputTnfaIggrabSig GM51 TNF Inpt IgR Input GM18951 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000777 777 GSM935448 Snyder Stanford hg18 input wgEncodeSydhTfbsGm18951InputTnfaIggrabSig TNFa Signal lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM18951 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18951InputIggmusSig GM51 Inpt IgM Input GM18951 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000737 737 GSM935528 Snyder Stanford hg18 input wgEncodeSydhTfbsGm18951InputIggmusSig None Signal lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM18951 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18951Pol2IggmusSig GM51 Pol2 IgM Pol2 GM18951 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000739 739 GSM935530 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18951Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM18951 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18951NfkbTnfaIggrabSig GM51 TNF NKB IgR NFKB GM18951 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000738 738 GSM935531 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18951NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM18951 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18526InputTnfaIggrabSig GM26 TNF Inpt IgR Input GM18526 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000776 776 GSM935449 Snyder Stanford hg18 input wgEncodeSydhTfbsGm18526InputTnfaIggrabSig TNFa Signal lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM18526 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18526InputIggmusSig GM26 Inpt IgM Input GM18526 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000732 732 GSM935525 Snyder Stanford hg18 input wgEncodeSydhTfbsGm18526InputIggmusSig None Signal lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM18526 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18526Pol2IggmusSig GM26 Pol2 IgM Pol2 GM18526 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000733 733 GSM935524 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18526Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM18526 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18526NfkbTnfaIggrabSig GM26 TNF NKB IgR NFKB GM18526 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000716 716 GSM935281 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18526NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM18526 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18505InputTnfaIggrabSig GM05 TNF Inpt IgR Input GM18505 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000775 775 GSM935446 Snyder Stanford hg18 input wgEncodeSydhTfbsGm18505InputTnfaIggrabSig TNFa Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM18505 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18505InputIggmusSig GM05 Inpt IgM Input GM18505 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000730 730 GSM935523 Snyder Stanford hg18 input wgEncodeSydhTfbsGm18505InputIggmusSig None Signal lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM18505 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18505Pol2IggmusSig GM05 Pol2 IgM Pol2 GM18505 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000731 731 GSM935522 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18505Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM18505 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18505NfkbTnfaIggrabSig GM05 TNF NKB IgR NFKB GM18505 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000715 715 GSM935282 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18505NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM18505 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm15510InputTnfaIggrabSig GM10 TNF Inpt IgR Input GM15510 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000774 774 GSM935447 Snyder Stanford hg18 input wgEncodeSydhTfbsGm15510InputTnfaIggrabSig TNFa Signal lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM15510 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm15510InputIggmusSig GM10 Inpt IgM Input GM15510 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000713 713 GSM935284 Snyder Stanford hg18 input wgEncodeSydhTfbsGm15510InputIggmusSig None Signal lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM15510 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm15510Pol2IggmusSig GM10 Pol2 IgM Pol2 GM15510 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000714 714 GSM935291 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm15510Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM15510 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm15510NfkbTnfaIggrabSig GM10 TNF NKB IgR NFKB GM15510 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000736 736 GSM935529 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm15510NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM15510 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12892InputTnfaIggrabSig GM92 TNF Inpt IgR Input GM12892 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000773 773 GSM935452 Snyder Stanford hg18 input wgEncodeSydhTfbsGm12892InputTnfaIggrabSig TNFa Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM12892 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12892InputIggmusSig GM92 Inpt IgM Input GM12892 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000711 711 GSM935286 Snyder Stanford hg18 input wgEncodeSydhTfbsGm12892InputIggmusSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12892 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12892Pol2IggmusSig GM92 Pol2 IgM Pol2 GM12892 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000729 729 GSM935640 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12892Pol2IggmusSig None Signal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12892 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12892NfkbTnfaIggrabSig GM92 TNF NKB IgR NFKB GM12892 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000712 712 GSM935285 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12892NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM12892 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12891InputTnfaIggrabSig GM91 TNF Inpt IgR Input GM12891 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000772 772 GSM935453 Snyder Stanford hg18 input wgEncodeSydhTfbsGm12891InputTnfaIggrabSig TNFa Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM12891 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12891InputIggmusSig GM91 Inpt IgM Input GM12891 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000709 709 GSM935387 Snyder Stanford hg18 input wgEncodeSydhTfbsGm12891InputIggmusSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12891 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12891Pol2IggmusSig GM91 Pol2 IgM Pol2 GM12891 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000710 710 GSM935287 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12891Pol2IggmusSig None Signal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12891 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12891NfkbTnfaIggrabSig GM91 TNF NKB IgR NFKB GM12891 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000735 735 GSM935526 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12891NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM12891 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm10847InputTnfaIggrabSig GM47 TNF Inpt IgR Input GM10847 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000770 770 GSM935451 Snyder Stanford hg18 input wgEncodeSydhTfbsGm10847InputTnfaIggrabSig TNFa Signal lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM10847 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm10847InputIggmusSig GM47 Inpt IgM Input GM10847 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000728 728 GSM935639 Snyder Stanford hg18 input wgEncodeSydhTfbsGm10847InputIggmusSig None Signal lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM10847 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm10847Pol2IggmusSig GM47 Pol2 IgM Pol2 GM10847 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000705 705 GSM935389 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm10847Pol2IggmusSig None Signal RNA Polymerase II lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM10847 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm10847NfkbTnfaIggrabSig GM47 TNF NKB IgR NFKB GM10847 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000734 734 GSM935527 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm10847NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM10847 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm08714InputUcdSig GM14 Inpt UCD Input GM08714 UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-04-19 2013-01-19 wgEncodeEH002870 2870 GSM935607 Snyder USC PeakSeq1.0 input wgEncodeSydhTfbsGm08714InputUcdSig None Signal lymphoblastoid cell line, Instability of heterochromatin of chromosomes 1, 9, and 16 with variable combined immunodeficiency; dysmorphic facial features, developmental delay, malabsorption, and recurrent infections; see GM08747 Fibroblast; donor subject is a compound heterozygote: one allele has a G&gt;A transition at nucleotide 1807 (1807G&gt;A) of the DNMT3B gene resulting in an Ala to Thr substitution at codon 603 [Ala603Thr (A603T)], the mutation occurring in a region between motifs I and IV within the catalytic domain of DNMT3B; the second allele has a G&gt;A transition within intron 22 located 11 nucleotides 5-prime of the normal splice acceptor site [IVS22AS,G&gt;A,-11] resulting in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA. This results in the insertion of 3 amino acids (serine, threonine, and proline) at codon 744 (744ins3). The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal GM08714 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm08714Znf274UcdSig GM14 Z274 UCD ZNF274 GM08714 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002866 2866 GSM935329 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsGm08714Znf274UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. lymphoblastoid cell line, Instability of heterochromatin of chromosomes 1, 9, and 16 with variable combined immunodeficiency; dysmorphic facial features, developmental delay, malabsorption, and recurrent infections; see GM08747 Fibroblast; donor subject is a compound heterozygote: one allele has a G&gt;A transition at nucleotide 1807 (1807G&gt;A) of the DNMT3B gene resulting in an Ala to Thr substitution at codon 603 [Ala603Thr (A603T)], the mutation occurring in a region between motifs I and IV within the catalytic domain of DNMT3B; the second allele has a G&gt;A transition within intron 22 located 11 nucleotides 5-prime of the normal splice acceptor site [IVS22AS,G&gt;A,-11] resulting in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA. This results in the insertion of 3 amino acids (serine, threonine, and proline) at codon 744 (744ins3). The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal GM08714 ZNF274 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshInputIggrabSig SKSH Inpt IgR Input SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-14 2013-05-14 wgEncodeEH003393 3393 GSM1003624 Snyder Stanford PeakSeq1.0 input wgEncodeSydhTfbsSknshInputIggrabSig None Signal neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshSmc3IggrabSig SKSH SMC3 IgR SMC3_(ab9263) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003377 3377 GSM1003627 Snyder Stanford exp wgEncodeSydhTfbsSknshSmc3IggrabSig None Signal Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH SMC3 (ab9263) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshRfx5IggrabSig SKSH RFX5 IgR RFX5_(200-401-194) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003375 3375 GSM1003629 Snyder Stanford exp wgEncodeSydhTfbsSknshRfx5IggrabSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH RFX5 (200-401-194) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshRad21IggrabSig SKSH Rad21 IgR Rad21 SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003376 3376 GSM1003628 Snyder Stanford exp wgEncodeSydhTfbsSknshRad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshP300bIggrabSig SKSH p300 IgR p300_(SC-584) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003378 3378 GSM1003626 Snyder Stanford exp wgEncodeSydhTfbsSknshP300bIggrabSig None Signal Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH p300 (SC-584) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshNrf1IggrabSig SKSH Nrf1 IgR Nrf1 SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003374 3374 GSM1003630 Snyder Stanford exp wgEncodeSydhTfbsSknshNrf1IggrabSig None Signal NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH Nrf1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshMxi1IggrabSig SKSH Mxi1 IgR Mxi1_(AF4185) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003373 3373 GSM1003631 Snyder Stanford exp wgEncodeSydhTfbsSknshMxi1IggrabSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH Mxi1 (AF4185) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshJundIggrabSig SKSH JunD IgR JunD SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003372 3372 GSM1003632 Snyder Stanford exp wgEncodeSydhTfbsSknshJundIggrabSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH JunD IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshCtcfbIggrabSig SKSH CTCF IgR CTCF_(SC-15914) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003371 3371 GSM1003633 Snyder Stanford exp wgEncodeSydhTfbsSknshCtcfbIggrabSig None Signal Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal SK-N-SH CTCF (SC-15914) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7InputUcdSig MCF7 Inpt UCD Input MCF-7 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000762 762 GSM935485 Snyder USC hg18 input wgEncodeSydhTfbsMcf7InputUcdSig None Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Znf217UcdSig MCF7 Z217 UCD ZNF217 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-08-03 2012-05-03 wgEncodeEH002036 2036 GSM935563 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf7Znf217UcdSig None Signal ZNF217 is an important oncogene based on the high frequency of amplification and overexpression in many cancer types, but its molecular mode of gene regulation is poorly understood. ZNF217 has been purified in complexes that contain repressor proteins such as CtBP2, suggesting that it acts as a transcriptional repressor. ZNF217 contains seven C2H2 zinc finger domains and has been shown to bind to gene promoters mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 ZNF217 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Tcf7l2UcdSig MCF7 TCF7L2 UCD TCF7L2 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-20 2012-06-19 wgEncodeEH002072 2072 GSM816438 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf7Tcf7l2UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 TCF7L2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Hae2f1UcdSig MCF7 HAE2 UCD HA-E2F1 MCF-7 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000693 693 GSM935477 Snyder USC hg18 exp wgEncodeSydhTfbsMcf7Hae2f1UcdSig None Signal The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 HA-E2F1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Gata3sc269UcdSig MCF7 GAT3 UCD GATA3_(SC-269) MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002812 2812 GSM935445 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsMcf7Gata3sc269UcdSig None Signal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 GATA3 SC269 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Gata3UcdSig MCF7 GAT3 UCD GATA3_(SC-268) MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-08-03 2012-05-03 wgEncodeEH002035 2035 GSM825711 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf7Gata3UcdSig None Signal This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal MCF-7 GATA3 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90InputIggrabSig IMR90 Inpt IgR Input IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002808 2808 GSM935512 Snyder Stanford PeakSeq1.0 input wgEncodeSydhTfbsImr90InputIggrabSig None Signal fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Rfx5IggrabSig IMR90 RFX5 IgR RFX5_(200-401-194) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003367 3367 GSM1003615 Snyder Stanford exp wgEncodeSydhTfbsImr90Rfx5IggrabSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 RFX5 (200-401-194) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Rad21IggrabSig IMR90 Rad2 IgR Rad21 IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002810 2810 GSM935624 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90Rad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Pol2IggrabSig IMR90 Pol2 IgR Pol2 IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002809 2809 GSM935513 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90Pol2IggrabSig None Signal RNA Polymerase II fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 Pol2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Mxi1IggrabSig IMR90 Mxi1 IgR Mxi1_(AF4185) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003366 3366 GSM1003614 Snyder Stanford exp wgEncodeSydhTfbsImr90Mxi1IggrabSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 Mxi1 (AF4185) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Mazab85725IggrabSig IMR90 MAZ IgR MAZ_(ab85725) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003365 3365 GSM1003613 Snyder Stanford exp wgEncodeSydhTfbsImr90Mazab85725IggrabSig None Signal May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 MAZ (ab85725) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90MafkIggrabSig IMR90 MafK IgR MafK_(ab50322) IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002832 2832 GSM935403 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90MafkIggrabSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 MafK IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90CtcfbIggrabSig IMR90 CTCF IgR CTCF_(SC-15914) IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002831 2831 GSM935404 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90CtcfbIggrabSig None Signal Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 CTCF IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Corestsc30189IggrabSig IMR90 COREST IgR COREST_(sc-30189) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003364 3364 GSM1003612 Snyder Stanford exp wgEncodeSydhTfbsImr90Corestsc30189IggrabSig None Signal Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 COREST (SC-30189) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Chd1nb10060411IggrabSig IMR90 CHD1 IgR CHD1_(NB100-60411) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003390 3390 GSM1003623 Snyder Stanford exp wgEncodeSydhTfbsImr90Chd1nb10060411IggrabSig None Signal ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 CHD1 (NB100-60411) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90CebpbIggrabSig IMR90 CBPB IgR CEBPB IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002807 2807 GSM935519 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90CebpbIggrabSig None Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal IMR90 CEBPB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecInputUcdSig HUVEC Inpt UCD Input HUVEC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001759 1759 GSM935346 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsHuvecInputUcdSig None Signal umbilical vein endothelial cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HUVEC Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecInputStdSig HUVEC Inpt Std Input HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000780 780 GSM935510 Snyder Yale hg18 input wgEncodeSydhTfbsHuvecInputStdSig None Signal umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HUVEC Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecPol2StdSig HUVEC Pol2 Std Pol2 HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000702 702 GSM935393 Snyder Stanford hg18 exp wgEncodeSydhTfbsHuvecPol2StdSig None Signal RNA Polymerase II umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HUVEC Pol2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecMaxStdSig HUVEC Max Std Max HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000768 768 GSM935572 Snyder Stanford hg18 exp wgEncodeSydhTfbsHuvecMaxStdSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HUVEC Max Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecGata2UcdSig HUVEC GAT2 UCD GATA-2 HUVEC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001758 1758 GSM935347 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHuvecGata2UcdSig None Signal GATA binding protein 2 umbilical vein endothelial cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HUVEC GATA2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecCjunStdSig HUVEC cJun Std c-Jun HUVEC std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000719 719 GSM935278 Snyder Stanford hg18 exp wgEncodeSydhTfbsHuvecCjunStdSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HUVEC c-Jun Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecCfosUcdSig HUVEC cFOS UCD c-Fos HUVEC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001774 1774 GSM935585 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHuvecCfosUcdSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. umbilical vein endothelial cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HUVEC c-FOS UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2InputUcdSig HEPG Inpt UCD Input HepG2 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000674 674 GSM817343 Snyder USC hg18 input wgEncodeSydhTfbsHepg2InputUcdSig None Signal hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEPG2 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2InputPravastStdSig HEPG prav Inpt Sd Input HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000640 640 GSM935313 Snyder Yale hg18 input wgEncodeSydhTfbsHepg2InputPravastStdSig pravastatin Signal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Signal HEPG2 Input Standard pravastatin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2InputInslnStdSig HEPG isln Inpt Sd Input HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000756 756 GSM935443 Snyder Stanford hg18 input wgEncodeSydhTfbsHepg2InputInslnStdSig insulin Signal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University DMEM with 0.5% BSA supplemented with 100 nM insulin and 10 uM 22-hydroxycholesterol for 6 h. (Snyder) Signal HEPG2 Input Standard insulin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2InputForsklnStdSig HEPG frsk Inpt Sd Input HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000755 755 GSM935444 Snyder Stanford hg18 input wgEncodeSydhTfbsHepg2InputForsklnStdSig forskolin Signal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 Input Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2InputIggrabSig HEPG Inpt IgR Input HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001791 1791 GSM935604 Snyder Stanford PeakSeq1.0 hg19 input wgEncodeSydhTfbsHepg2InputIggrabSig None Signal hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2InputIgggoatSig HEPG Inpt IgG Input HepG2 IgG-goat ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002803 2803 GSM935515 Snyder Stanford PeakSeq1.0 input wgEncodeSydhTfbsHepg2InputIgggoatSig None Signal hepatocellular carcinoma Input signal from Normal Goat IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Input IgG-goat ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Znf274UcdSig HEPG Z274 UCD ZNF274 HepG2 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001755 1755 GSM935350 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Znf274UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEPG2 ZNF274 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Usf2IggrabSig HEPG USF2 IgR USF2 HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001804 1804 GSM935646 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Usf2IggrabSig None Signal Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 USF2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Tr4UcdSig HEPG TR4 UCD TR4 HepG2 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000675 675 GSM935596 Snyder USC hg18 exp wgEncodeSydhTfbsHepg2Tr4UcdSig None Signal (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEPG2 TR4 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Tcf7l2UcdSig HEPG TCF7L2 UCD TCF7L2 HepG2 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2001-06-27 2011-01-19 2011-10-19 wgEncodeEH001780 1780 GSM782122 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Tcf7l2UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HEPG2 TCF7L2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2TbpIggrabSig HEPG TBP IgR TBP HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001793 1793 GSM935280 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2TbpIggrabSig None Signal General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 TBP IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Srebp2PravastStdSig HEPG prav SBP2 Sd SREBP2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000643 643 GSM935314 Snyder Yale hg18 exp wgEncodeSydhTfbsHepg2Srebp2PravastStdSig pravastatin Signal Sterol regulatory element binding transcription factor 2 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Signal HEPG2 SREBP2 Standard pravastatin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Srebp1PravastStdSig HEPG prav SRBP Sd SREBP1 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000642 642 GSM935315 Snyder Yale hg18 exp wgEncodeSydhTfbsHepg2Srebp1PravastStdSig pravastatin Signal Sterol regulatory element binding transcription factor 1 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Signal HEPG2 SREBP1 Standard pravastatin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Srebp1InslnStdSig HEPG isln SRBP Sd SREBP1 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000759 759 GSM935627 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Srebp1InslnStdSig insulin Signal Sterol regulatory element binding transcription factor 1 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University DMEM with 0.5% BSA supplemented with 100 nM insulin and 10 uM 22-hydroxycholesterol for 6 h. (Snyder) Signal HEPG2 SREBP1 Standard insulin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Smc3ab9263IggrabSig HEPG SMC3 IgR SMC3_(ab9263) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001861 1861 GSM935542 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Smc3ab9263IggrabSig None Signal Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 SMC3 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Rfx5200401194IggrabSig HEPG RFX5 IgR RFX5_(200-401-194) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001843 1843 GSM935304 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Rfx5200401194IggrabSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 RFX5 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Rad21IggrabSig HEPG Rad2 IgR Rad21 HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001803 1803 GSM935647 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Rad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2s2IggrabSig HEPG PolS IgR Pol2(phosphoS2) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001860 1860 GSM935543 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Pol2s2IggrabSig None Signal RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Pol2 S2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2PravastStdSig HEPG prav Pol2 Sd Pol2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000641 641 GSM935312 Snyder Yale hg18 exp wgEncodeSydhTfbsHepg2Pol2PravastStdSig pravastatin Signal RNA Polymerase II hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Signal HEPG2 Pol2 Standard pravastatin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2ForsklnStdSig HEPG frsk Pol2 Sd Pol2 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000758 758 GSM935628 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Pol2ForsklnStdSig forskolin Signal RNA Polymerase II hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 Pol2 Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2IggrabSig HEPG Pol2 IgR Pol2 HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001792 1792 GSM935603 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Pol2IggrabSig None Signal RNA Polymerase II hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Pol2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pgc1aForsklnStdSig HEPG frsk PGC1 Sd PGC1A HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000757 757 GSM935623 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Pgc1aForsklnStdSig forskolin Signal The protein encoded by this gene is a transcriptional coactivator that regulates the genes involved in energy metabolism. This protein interacts with PPARgamma, which permits the interaction of this protein with multiple transcription factors. This protein can interact with, and regulate the activities of, cAMP response element binding protein (CREB) and nuclear respiratory factors (NRFs). hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 PGC1A Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2P300sc582IggrabSig HEPG p300 IgR p300_(SC-584) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001862 1862 GSM935545 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2P300sc582IggrabSig None Signal Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 p300 SC584 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Nrf1IggrabSig HEPG Nrf1 IgR Nrf1 HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001802 1802 GSM935648 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Nrf1IggrabSig None Signal NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Nrf1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mafksc477IggrabSig HEPG MafK IgR MafK_(SC-477) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH001850 1850 GSM935610 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Mafksc477IggrabSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 MafK SC477 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mxi1StdSig HEPG Mxi1 Std Mxi1_(AF4185) HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002029 2029 GSM935437 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Mxi1StdSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Mxi1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mazab85725IggrabSig HEPG MAZ IgR MAZ_(ab85725) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002860 2860 GSM935335 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2Mazab85725IggrabSig None Signal May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 MAZ IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2MaxIggrabSig HEPG Max IgR Max HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002796 2796 GSM935406 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2MaxIggrabSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 Max IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mafkab50322IggrabSig HEPG MafK IgR MafK_(ab50322) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001842 1842 GSM935305 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Mafkab50322IggrabSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 MafK IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Maffm8194IggrabSig HEPG MafF IgR MafF_(M8194) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001841 1841 GSM935306 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Maffm8194IggrabSig None Signal The protein encoded by this gene is a (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. Can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. May also be involved in the cellular stress response. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 MafF IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2JundIggrabSig HEPG JunD IgR JunD HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001801 1801 GSM935649 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2JundIggrabSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 JunD IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Irf3IggrabSig HEPG IRF3 IgR IRF3 HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001800 1800 GSM935650 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Irf3IggrabSig None Signal Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 IRF3 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Hsf1ForsklnStdSig HEPG frsk HSF1 Sd HSF1 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000754 754 GSM935626 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Hsf1ForsklnStdSig forskolin Signal Epitope corresponding to amino acids 219-529 of heat shock transcription factor 1 (HSF1) of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 HSF1 Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Hnf4aForsklnStdSig HEPG frsk HNF4 Sd HNF4A HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000753 753 GSM935619 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Hnf4aForsklnStdSig forskolin Signal Epitope mapping at the C-terminus of Rab 11 of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 HNF4A Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Grp20ForsklnStdSig HEPG frsk GR20 Sd GRp20 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000752 752 GSM935620 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Grp20ForsklnStdSig forskolin Signal Epitope mapping at the C-terminus of GR alpha of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 GRp20 Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2ErraForsklnStdSig HEPG frsk ERRA Sd ERRA HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000751 751 GSM935621 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2ErraForsklnStdSig forskolin Signal Epitope corresponding to amino acids 81-160 mapping near the N-terminus of ERRalpha of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 ERRA Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Corestsc30189IggrabSig HEPG COREST IgR COREST_(sc-30189) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002845 2845 GSM935579 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2Corestsc30189IggrabSig None Signal Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 COREST SC30189 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CjunIggrabSig HEPG cJun IgR c-Jun HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001794 1794 GSM935364 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2CjunIggrabSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 c-Jun IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Chd2ab68301IggrabSig HEPG CHD2 IgR CHD2_(AB68301) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001840 1840 GSM935307 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Chd2ab68301IggrabSig None Signal CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 CHD2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CebpzIggrabSig HEPG CEBPZ IgR CEBPZ HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002859 2859 GSM935274 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2CebpzIggrabSig None Signal Stimulates transcription from the HSP70 promoter. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 CEBPZ IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CebpbForsklnStdSig HEPG frsk CBPB Sd CEBPB HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000750 750 GSM935622 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2CebpbForsklnStdSig forskolin Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Signal HEPG2 CEBPB Standard forskolin ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CebpbIggrabSig HEPG CBPB IgR CEBPB HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-04 2011-01-14 2011-10-13 wgEncodeEH001829 1829 GSM935493 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2CebpbIggrabSig None Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 CEBPB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Brca1a300IggrabSig HEPG BRC1 IgR BRCA1_(A300-000A) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001859 1859 GSM935609 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Brca1a300IggrabSig None Signal Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 BRCA1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Bhlhe40cIggrabSig HEPG BHL4 IgR BHLHE40_(NB100-1800) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002032 2032 GSM935566 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Bhlhe40cIggrabSig None Signal This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 BHLHE40 NB100 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Arid3anb100279IggrabSig HEPG ARI3 IgR ARID3A_(NB100-279) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002858 2858 GSM935275 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2Arid3anb100279IggrabSig None Signal This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. (provided by RefSeq) hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HEPG2 ARID3A NB100279 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputUcdSig HeLa Inpt UCD Input HeLa-S3 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001754 1754 GSM818744 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsHelas3InputUcdSig None Signal cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputStdSig HeLa Inpt Std Input HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000612 612 GSM817342 Snyder Yale hg18 input wgEncodeSydhTfbsHelas3InputStdSig None Signal cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputIfng30StdSig HeLa IFg3 Inpt Sd Input HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000611 611 GSM935357 Snyder Yale hg18 input wgEncodeSydhTfbsHelas3InputIfng30StdSig IFNg30 Signal cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Signal HeLa-S3 Input Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputNakeddnaSig HeLa Inpt NDNA Input HeLa-S3 Naked_DNA ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000636 636 GSM935538 Snyder Yale hg18 input wgEncodeSydhTfbsHelas3InputNakeddnaSig None Signal cervical carcinoma Control signal from Naked DNA. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Input Naked DNA ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputMnaseSig HeLa Inpt MNas Input HeLa-S3 MNase ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000635 635 GSM935537 Snyder Yale hg18 input wgEncodeSydhTfbsHelas3InputMnaseSig None Signal cervical carcinoma Input signal from MNase digested DNA. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Input MNase ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputLargefragmentSig HeLa Inpt LFrg Input HeLa-S3 Large_Fragment ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000634 634 GSM935536 Snyder Yale hg18 input wgEncodeSydhTfbsHelas3InputLargefragmentSig None Signal cervical carcinoma Control signal from sonication into large fragments of DNA (350-800 bp). Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Input Large Fragment ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputIggrabSig HeLa Inpt IgR Input HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000744 744 GSM935339 Snyder Stanford hg18 input wgEncodeSydhTfbsHelas3InputIggrabSig None Signal cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3InputIggmusSig HeLa Inpt IgM Input HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000633 633 GSM935535 Snyder Yale hg18 input wgEncodeSydhTfbsHelas3InputIggmusSig None Signal cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Zzz3StdSig HeLa ZZZ3 Std ZZZ3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-17 2011-05-17 wgEncodeEH001872 1872 GSM935416 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Zzz3StdSig None Signal ZZZ3 contains one ZZ-type zinc finger domain. ZZ type finger domains are named because of their ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions -they are most likely involved in ligand binding or molecular scaffolding. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 ZZZ3 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Znf274UcdSig HeLa Z274 UCD ZNF274 HeLa-S3 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-08-17 2011-05-17 wgEncodeEH001763 1763 GSM935459 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Znf274UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 ZNF274 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Znf143IggrabSig HeLa Z143 IgR Znf143_(16618-1-AP) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002028 2028 GSM935436 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Znf143IggrabSig None Signal Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Znf143 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Zkscan1hpa006672IggrabSig HeLa ZKSCN1 IgR ZKSCAN1_(HPA006672) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002857 2857 GSM935362 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Zkscan1hpa006672IggrabSig None Signal The ZKSCAN1 gene encodes a transcriptional regulator of the KRAB (Kruppel-associated box) subfamily of zinc finger proteins, which contain repeated Cys2-His2 (C2H2) zinc finger domains that are connected by conserved sequences, called H/C links. Transcriptional regulatory proteins containing tandemly repeated zinc finger domains are thought to be involved in both normal and abnormal cellular proliferation and differentiation. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 ZKSCAN1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Usf2IggmusSig HeLa USF2 IgM USF2 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001819 1819 GSM935561 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Usf2IggmusSig None Signal Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 USF2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tr4StdSig HeLa TR4 Std TR4 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000687 687 GSM935369 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Tr4StdSig None Signal (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 TR4 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tf3c110StdSig HeLa TF3C Std TFIIIC-110 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000747 747 GSM935342 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Tf3c110StdSig None Signal TFIIIC-110 is a subunit of the RNA Polymerase III transcription factor TFIIIC. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 TFIIIC-110 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tcf7l2c9b92565UcdSig HeLa TCF7L2 UCD TCF7L2_C9B9_(2565) HeLa-S3 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-12-19 2012-09-18 wgEncodeEH002813 2813 GSM935625 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Tcf7l2c9b92565UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 TCF7L2 C9B9 2565 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tcf7l2UcdSig HeLa TCF7L2 UCD TCF7L2 HeLa-S3 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002069 2069 GSM816436 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Tcf7l2UcdSig None Signal TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 TCF7L2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3TbpIggrabSig HeLa TBP IgR TBP HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001790 1790 GSM935606 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3TbpIggrabSig None Signal General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 TBP IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Stat3IggrabSig HeLa STA3 IgR STAT3 HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001799 1799 GSM935276 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Stat3IggrabSig None Signal Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 STAT3 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Stat1Ifng30StdSig HeLa IFg3 STA1 Sd STAT1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000614 614 GSM935360 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3Stat1Ifng30StdSig IFNg30 Signal transcription factor, activated by interferon signalling cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Signal HeLa-S3 STAT1 Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Spt20StdSig HeLa SPT Std SPT20 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001855 1855 GSM935615 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Spt20StdSig None Signal Also known as FAM48A or P38IP. It is a component of SAGA complex. Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down-regulation of E-cadherin during gastrulation by regulating E-cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by Fgf signaling and Snail. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 SPT20 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Smc3ab9263IggrabSig HeLa SMC3 IgR SMC3_(ab9263) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001839 1839 GSM935384 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Smc3ab9263IggrabSig None Signal Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 SMC3 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Rpc155StdSig HeLa RPC1 Std RPC155 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000766 766 GSM935489 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Rpc155StdSig None Signal polymerase (RNA) III (DNA directed) polypeptide A, 155kDa cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 RPC155 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Rfx5200401194IggrabSig HeLa RFX5 IgR RFX5_(200-401-194) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001818 1818 GSM935560 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Rfx5200401194IggrabSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 RFX5 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Rad21IggrabSig HeLa Rad2 IgR Rad21 HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001789 1789 GSM935571 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Rad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Prdm19115IggrabSig HeLa PRDM IgR PRDM1_(9115) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001817 1817 GSM935555 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Prdm19115IggrabSig None Signal Transcriptional repressor that binds specifically to the PRDI element in the promoter of the beta-interferon gene. Drives the maturation of B-lymphocytes into Ig secreting cells. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 PRDM1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Pol2s2IggrabSig HeLa PolS IgR Pol2(phosphoS2) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001838 1838 GSM935383 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Pol2s2IggrabSig None Signal RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Pol2 S2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Pol2StdSig HeLa Pol2 Std Pol2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000613 613 GSM935395 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3Pol2StdSig None Signal RNA Polymerase II cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Pol2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3P300sc584sc584IggrabSig HeLa p300 IgR p300_(SC-584) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001820 1820 GSM935500 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3P300sc584sc584IggrabSig None Signal Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 p300 SC584 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Nrf1IggmusSig HeLa Nrf1 IgM Nrf1 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000723 723 GSM935636 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Nrf1IggmusSig None Signal NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Nrf1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3NfybIggrabSig HeLa NYB IgR NF-YB HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002067 2067 GSM935408 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3NfybIggrabSig None Signal NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 NF-YB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3NfyaIggrabSig HeLa NYA IgR NF-YA HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002066 2066 GSM935508 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3NfyaIggrabSig None Signal NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 NF-YA IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Mxi1af4185IggrabSig HeLa Mxi1 IgR Mxi1_(AF4185) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001826 1826 GSM935498 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Mxi1af4185IggrabSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Mxi1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Mazab85725IggrabSig HeLa MAZ IgR MAZ_(ab85725) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002855 2855 GSM935272 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Mazab85725IggrabSig None Signal May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 MAZ IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3MaxStdSig HeLa Max Std Max HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000646 646 GSM935318 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3MaxStdSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 Max Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3MaxIggrabSig HeLa Max IgR Max HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002830 2830 GSM935405 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3MaxIggrabSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 Max IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3MafkIggrabSig HeLa MafK IgR MafK_(ab50322) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002856 2856 GSM935290 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3MafkIggrabSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 MafK IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3JundIggrabSig HeLa JunD IgR JunD HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000745 745 GSM935328 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3JundIggrabSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 JunD IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Irf3IggrabSig HeLa IRF3 IgR IRF3 HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001788 1788 GSM935570 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Irf3IggrabSig None Signal Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 IRF3 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Ini1IggmusSig HeLa INI1 IgM Ini1 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000722 722 GSM935635 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Ini1IggmusSig None Signal Ini1 (BAF47, SMARCB1) is a ubiquitous 47 kD component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 INI1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Hcfc1nb10068209IggrabSig HeLa-S3 HCFC1 IgR HCFC1_(NB100-68209) HeLa-S3 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003389 3389 GSM1003618 Snyder Stanford exp wgEncodeSydhTfbsHelas3Hcfc1nb10068209IggrabSig None Signal The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 HCFC1 (NB100-68209) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Hae2f1StdSig HeLa HAE2 Std HA-E2F1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000688 688 GSM935366 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Hae2f1StdSig None Signal The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 HA-E2F1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Gtf2f1ab28179IggrabSig HeLa GT2F IgR GTF2F1_(AB28179) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001816 1816 GSM935554 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Gtf2f1ab28179IggrabSig None Signal RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 GTF2F1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Gcn5StdSig HeLa GCN5 Std GCN5 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001849 1849 GSM935302 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Gcn5StdSig None Signal KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4 cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 GCN5 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Elk4UcdSig HeLa ELK4 UCD ELK4 HeLa-S3 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001753 1753 GSM935351 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Elk4UcdSig None Signal This gene is a member of the Ets family of transcription factors and of the ternary complex factor (TCF) subfamily. (provided by RefSeq) cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 ELK4 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Elk112771IggrabSig HeLa ELK1 IgR ELK1_(1277-1) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-12-01 wgEncodeEH002864 2864 GSM935326 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Elk112771IggrabSig None Signal Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 ELK1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3E2f6StdSig HeLa E2F6 Std E2F6 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000692 692 GSM935476 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3E2f6StdSig None Signal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 E2F6 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3E2f4StdSig HeLa E2F4 Std E2F4 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000689 689 GSM935365 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3E2f4StdSig None Signal mapping at the C-terminus of E2F4 of human origin cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 E2F4 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3E2f1StdSig HeLa E2F1 Std E2F1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000699 699 GSM935484 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3E2f1StdSig None Signal E2F1, the original member of the E2F family of transcription factors, was identified as a cellular protein with DNA binding activity associated with the adenovirus E2 gene promoter. E2F1 is cell cycle regulated with very low levels in early G1, then increasing levels as cells move from G1 to S, and highest levels of protein at the G1/S boundary, which is consistent with its role in S-phase entry. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 E2F1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Corestsc30189IggrabSig HeLa COREST IgR COREST_(sc-30189) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002844 2844 GSM935578 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Corestsc30189IggrabSig None Signal Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 COREST SC30189 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CmycStdSig HeLa cMyc Std c-Myc HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000648 648 GSM935320 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3CmycStdSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 c-Myc Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CjunIggrabSig HeLa cJun IgR c-Jun HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000746 746 GSM935341 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3CjunIggrabSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 c-Jun IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Chd2IggrabSig HeLa CHD2 IgR CHD2_(AB68301) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002027 2027 GSM935432 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Chd2IggrabSig None Signal CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 CHD2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CfosStdSig HeLa cFOS Std c-Fos HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000647 647 GSM935317 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3CfosStdSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 c-FOS Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CebpbIggrabSig HeLa CBPB IgR CEBPB HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001815 1815 GSM935553 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3CebpbIggrabSig None Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 CEBPB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brg1IggmusSig HeLa BRG1 IgM Brg1 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000781 781 GSM935511 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3Brg1IggmusSig None Signal Brg1 (SMARCA4) is an ATPase subunit of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Yale University Signal HeLa-S3 BRG1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brf2StdSig HeLa BRF2 Std BRF2 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000765 765 GSM935435 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Brf2StdSig None Signal Brf2 is a component of an alternate form of the RNA Polymerase III transcription factor TFIIIB. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 BRF2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brf1StdSig HeLa BRF1 Std BRF1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000764 764 GSM935582 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Brf1StdSig None Signal 'B-related factor 1', subunit of RNA polymerase III transcription initiation factor IIIB cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 BRF1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brca1a300IggrabSig HeLa BRC1 IgR BRCA1_(A300-000A) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001814 1814 GSM935552 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Brca1a300IggrabSig None Signal Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 BRCA1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Bdp1StdSig HeLa BDP1 Std BDP1 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000763 763 GSM935486 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Bdp1StdSig None Signal 'B double-prime 1', subunit of RNA polymerase III transcription initiation factor IIIB cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal HeLa-S3 BDP1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Baf170IggmusSig HeLa BAF7 IgM BAF170 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000721 721 GSM935638 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Baf170IggmusSig None Signal BAF170 (SMARCC2, Brg1-Associated Factor, 170 kD) is a ubiquitous component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 BAF170 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Baf155IggmusSig HeLa BAF5 IgM BAF155 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000720 720 GSM935637 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Baf155IggmusSig None Signal BAF155 (SMARCC1, Brg1-Associated Factor, 155 kD) is a ubiquitous component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal HeLa-S3 BAF155 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Ap2gammaStdSig HeLa AP2g Std AP-2gamma HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000686 686 GSM935370 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Ap2gammaStdSig None Signal Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes. AP-2 factors bind to the consensus sequence 5'-GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development. They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 AP-2g Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Ap2alphaStdSig HeLa AP2a Std AP-2alpha HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000685 685 GSM935367 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Ap2alphaStdSig None Signal Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes. AP-2 factors bind to the consensus sequence 5' -GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development. They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC. AP-2alpha is the only AP-2 protein required for early morphogenesis of the lens vesicle (by similarity). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal HeLa-S3 AP-2a Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549InputIggrabSig A549 Inpt IgR Input A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002819 2819 GSM935629 Snyder Stanford PeakSeq1.0 input wgEncodeSydhTfbsA549InputIggrabSig None Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549Rad21IggrabSig A549 Rad2 IgR Rad21 A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002822 2822 GSM935300 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549Rad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549Pol2s2IggrabSig A549 PolS IgR Pol2(phosphoS2) A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002821 2821 GSM935299 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549Pol2s2IggrabSig None Signal RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 Pol2 S2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549MaxIggrabSig A549 Max IgR Max A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002820 2820 GSM935298 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549MaxIggrabSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 Max IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549CtcfbIggrabSig A549 CTCF IgR CTCF_(SC-15914) A549 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003384 3384 GSM1003606 Snyder Stanford exp wgEncodeSydhTfbsA549CtcfbIggrabSig None Signal Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 CTCF (SC-15914) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549CmycIggrabSig A549 c-Myc IgR c-Myc A549 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003385 3385 GSM1003607 Snyder Stanford exp wgEncodeSydhTfbsA549CmycIggrabSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 c-Myc IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549CebpbIggrabSig A549 CBPB IgR CEBPB A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002818 2818 GSM935630 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549CebpbIggrabSig None Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 CEBPB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549Bhlhe40IggrabSig A549 BHL4 IgR BHLHE40 A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002817 2817 GSM935440 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549Bhlhe40IggrabSig None Signal This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal A549 BHLHE40 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputUcdSig K562 Inpt UCD Input K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000672 672 GSM935601 Snyder USC hg18 input wgEncodeSydhTfbsK562InputUcdSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputStdSig K562 Inpt Std Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000615 615 GSM935363 Snyder Yale hg18 input wgEncodeSydhTfbsK562InputStdSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputIfng6hStdSig K562 IFg6 Inpt Sd Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000658 658 GSM935427 Snyder Yale hg18 input wgEncodeSydhTfbsK562InputIfng6hStdSig IFNg6h Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Signal K562 Input Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputIfng30StdSig K562 IFg3 Inpt Sd Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000657 657 GSM935420 Snyder Yale hg18 input wgEncodeSydhTfbsK562InputIfng30StdSig IFNg30 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Signal K562 Input Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputIfna6hStdSig K562 IFa6 Inpt Sd Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000656 656 GSM935419 Snyder Yale hg18 input wgEncodeSydhTfbsK562InputIfna6hStdSig IFNa6h Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Signal K562 Input Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputIfna30StdSig K562 IFa3 Inpt Sd Input K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000655 655 GSM935422 Snyder Yale hg18 input wgEncodeSydhTfbsK562InputIfna30StdSig IFNa30 Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Signal K562 Input Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputIggrabSig K562 Inpt IgR Input K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001795 1795 GSM935618 Snyder Stanford PeakSeq1.0 hg19 input wgEncodeSydhTfbsK562InputIggrabSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562InputIggmusSig K562 Inpt IgM Input K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000726 726 GSM935631 Snyder Stanford hg18 input wgEncodeSydhTfbsK562InputIggmusSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znfmizdcp1ab65767IggrabSig K562 ZNF-MIZD IgR ZNF-MIZD-CP1_(ab65767) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003381 3381 GSM1003611 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Znfmizdcp1ab65767IggrabSig None Signal Zinc finger MIZ domain-containing protein 1 that increases ligand-dependent transcriptional activity of AR and promotes AR sumoylation. The stimulation of AR activity is dependent upon sumoylation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 ZNF-MIZD-CP1 (ab65767) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf384hpa004051IggrabSig K562 ZNF384 IgR ZNF384_(HPA004051) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003382 3382 GSM1003621 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Znf384hpa004051IggrabSig None Signal This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 ZNF384 (HPA004051) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf274m01UcdSig K562 Z274M UCD ZNF274_(M01) K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-14 2012-06-14 wgEncodeEH002068 2068 GSM935503 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Znf274m01UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor and interacts with the KAP1 corepressor complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 ZNF274 (M01) UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf274UcdSig K562 Z274 UCD ZNF274 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000696 696 GSM935479 Snyder USC hg18 exp wgEncodeSydhTfbsK562Znf274UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 ZNF274 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf263UcdSig K562 Z263 UCD ZNF263 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000630 630 GSM935532 Snyder USC hg18 exp wgEncodeSydhTfbsK562Znf263UcdSig None Signal ZNF263 (NP_005732, 201 a.a. ~ 299 a.a) partial recombinant protein with GST tag. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 ZNF263 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf143IggrabSig K562 Z143 IgR Znf143_(16618-1-AP) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002030 2030 GSM935568 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Znf143IggrabSig None Signal Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Znf143 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Zc3h11anb10074650IggrabSig K562 ZC3H11A IgR ZC3H11A_(NB100-74650) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003380 3380 GSM1003610 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Zc3h11anb10074650IggrabSig None Signal ZC3H11A is a C3H1-type zinc finger protein. ZC3H11A has been identified as a protein that is phosphorylated upon DNA damage by ATM or ATR. The function of ZC3H11A remains uncharacterized. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 ZC3H11A (NB100-74650) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Yy1UcdSig K562 YY1 UCD YY1 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000684 684 GSM935368 Snyder USC hg18 exp wgEncodeSydhTfbsK562Yy1UcdSig None Signal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 YY1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Xrcc4StdSig K562 XRCC Std XRCC4 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000650 650 GSM935425 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Xrcc4StdSig None Signal Recognizes the XRCC4 protein (X ray cross complementation protein). XRCC4 is a ubiquitous protein reported to have a role in DNA double-stranded break repair and in V(D)J recombination. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 XRCC4 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Usf2IggrabSig K562 USF2 IgR USF2 K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001797 1797 GSM935356 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Usf2IggrabSig None Signal Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 USF2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ubtfsab1404509IggmusSig K562 UBTF IgM UBTF_(SAB1404509) K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002850 2850 GSM935642 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Ubtfsab1404509IggmusSig None Signal Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 UBTF IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ubfsc13125IggmusSig K562 UBF IgM UBF_(sc-13125) K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002863 2863 GSM935338 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Ubfsc13125IggmusSig None Signal Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 UBF IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tr4UcdSig K562 TR4 UCD TR4 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000682 682 GSM935374 Snyder USC hg18 exp wgEncodeSydhTfbsK562Tr4UcdSig None Signal (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 TR4 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tf3c110StdSig K562 TF3C Std TFIIIC-110 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000748 748 GSM935343 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Tf3c110StdSig None Signal TFIIIC-110 is a subunit of the RNA Polymerase III transcription factor TFIIIC. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 TFIIIC-110 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562TbpIggmusSig K562 TBP IgM TBP K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001825 1825 GSM935495 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562TbpIggmusSig None Signal General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 TBP IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tblr1nb600270IggrabSig K562 TBLR1 IgR TBLR1_(NB600-270) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002848 2848 GSM935574 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Tblr1nb600270IggrabSig None Signal F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 TBLR1 NB600270 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tblr1ab24550IggrabSig K562 TBLR1 IgR TBLR1_(ab24550) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002849 2849 GSM935575 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Tblr1ab24550IggrabSig None Signal F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 TBLR1 AB24550 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tal1sc12984IggmusSig K562 TAL1 IgM TAL1_(SC-12984) K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001824 1824 GSM935496 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Tal1sc12984IggmusSig None Signal TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 TAL1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat2Ifna6hStdSig K562 IFa6 STA2 Sd STAT2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000666 666 GSM935469 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat2Ifna6hStdSig IFNa6h Signal peptide mapping at c-terminus of Human STAT2 p-113 (C-20) X leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Signal K562 STAT2 Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat2Ifna30StdSig K562 IFa3 STA2 Sd STAT2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000665 665 GSM935470 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat2Ifna30StdSig IFNa30 Signal peptide mapping at c-terminus of Human STAT2 p-113 (C-20) X leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Signal K562 STAT2 Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifng6hStdSig K562 IFg6 STA1 Sd STAT1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000761 761 GSM935488 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Stat1Ifng6hStdSig IFNg6h Signal transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 6 hours (Snyder) Signal K562 STAT1 Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifng30StdSig K562 IFg3 STA1 Sd STAT1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000760 760 GSM935487 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Stat1Ifng30StdSig IFNg30 Signal transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Signal K562 STAT1 Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifna6hStdSig K562 IFa6 STA1 Sd STAT1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000664 664 GSM935471 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat1Ifna6hStdSig IFNa6h Signal transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Signal K562 STAT1 Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifna30StdSig K562 IFa3 STA1 Sd STAT1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000663 663 GSM935472 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat1Ifna30StdSig IFNa30 Signal transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Signal K562 STAT1 Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Smc3ab9263IggrabSig K562 SMC3 IgR SMC3_(ab9263) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001845 1845 GSM935310 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Smc3ab9263IggrabSig None Signal Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 SMC3 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Sirt6StdSig K562 SIRT Std SIRT6 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000681 681 GSM935371 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Sirt6StdSig None Signal A synthetic peptide made to an internal region of the human SIRT6 protein leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 SIRT6 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Setdb1UcdSig K562 STDB UCD SETDB1 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000677 677 GSM935598 Snyder USC hg18 exp wgEncodeSydhTfbsK562Setdb1UcdSig None Signal SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 SETDB1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Setdb1MnasedUcdSig K562 MNas STDB UC SETDB1 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000769 769 GSM935573 Snyder USC hg18 exp wgEncodeSydhTfbsK562Setdb1MnasedUcdSig MNaseD Signal SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Fragmented using micrococcal nuclease digestion Signal K562 SETDB1 UC Davis MNaseD ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Rpc155StdSig K562 RPC1 Std RPC155 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000680 680 GSM935372 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Rpc155StdSig None Signal polymerase (RNA) III (DNA directed) polypeptide A, 155kDa leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 RPC155 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Rfx5IggrabSig K562 RFX5 IgR RFX5_(200-401-194) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002033 2033 GSM935565 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Rfx5IggrabSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 RFX5 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Rad21StdSig K562 Rad2 Std Rad21 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000649 649 GSM935319 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Rad21StdSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 Rad21 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol3StdSig K562 Pol3 Std Pol3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000694 694 GSM935481 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Pol3StdSig None Signal RNA Polymerase III leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 POL3 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2s2StdSig K562 PolS Std Pol2(phosphoS2) K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-07-12 2011-04-12 wgEncodeEH001805 1805 GSM935645 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Pol2s2StdSig None Signal RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Pol2 S2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2s2IggrabSig K562 PolS IgR Pol2(phosphoS2) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002833 2833 GSM935402 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Pol2s2IggrabSig None Signal RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Pol2 S2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2StdSig K562 Pol2 Std Pol2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000616 616 GSM935358 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2StdSig None Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 Pol2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifng6hStdSig K562 IFg6 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000662 662 GSM935473 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2Ifng6hStdSig IFNg6h Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Signal K562 Pol2 Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifng30StdSig K562 IFg3 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000704 704 GSM935388 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Pol2Ifng30StdSig IFNg30 Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Signal K562 Pol2 Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifna6hStdSig K562 IFa6 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000661 661 GSM935474 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2Ifna6hStdSig IFNa6h Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Signal K562 Pol2 Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifna30StdSig K562 IFa3 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000660 660 GSM935475 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2Ifna30StdSig IFNa30 Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Signal K562 Pol2 Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2IggmusSig K562 Pol2 IgM Pol2 K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000727 727 GSM935632 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Pol2IggmusSig None Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562P300sc584sc48343IggrabSig K562 p300 IgR p300_(SC-48343) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001828 1828 GSM935494 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562P300sc584sc48343IggrabSig None Signal Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 p300 SC48343 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562P300IggrabSig K562 p300 IgR p300 K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002834 2834 GSM935401 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562P300IggrabSig None Signal EP300(c-20) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 p300 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Nrf1IggrabSig K562 Nrf1 IgR Nrf1 K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001796 1796 GSM935361 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Nrf1IggrabSig None Signal NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Nrf1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562NfybStdSig K562 NYB Std NF-YB K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002024 2024 GSM935429 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562NfybStdSig None Signal NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 NF-YB Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562NfyaStdSig K562 NYA Std NF-YA K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-22 2012-03-22 wgEncodeEH002021 2021 GSM935433 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562NfyaStdSig None Signal NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 NF-YA Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Nfe2StdSig K562 NFE2 Std NF-E2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000624 624 GSM935414 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Nfe2StdSig None Signal Nuclear factor, erythroid-derived 2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 NF-E2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562NelfeStdSig K562 NELF Std NELFe K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000701 701 GSM935392 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562NelfeStdSig None Signal NELF-E (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 NELFe Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Mxi1af4185IggrabSig K562 Mxi1 IgR Mxi1_(AF4185) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001827 1827 GSM935497 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Mxi1af4185IggrabSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Mxi1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Mazab85725IggrabSig K562 MAZ IgR MAZ_(ab85725) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002862 2862 GSM935337 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Mazab85725IggrabSig None Signal May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 MAZ IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562MaxStdSig K562 Max Std Max K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000637 637 GSM935539 Snyder Yale hg18 exp wgEncodeSydhTfbsK562MaxStdSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 Max Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562MaxIggrabSig K562 Max IgR Max K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEH002869 2869 GSM935344 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562MaxIggrabSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Max IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Mafkab50322IggrabSig K562 MafK IgR MafK_(ab50322) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001844 1844 GSM935311 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Mafkab50322IggrabSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 MafK IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562MaffIggrabSig K562 MafF IgR MafF_(M8194) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002804 2804 GSM935520 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562MaffIggrabSig None Signal The protein encoded by this gene is a (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. Can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. May also be involved in the cellular stress response. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 MafF IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Kap1UcdSig K562 KAP1 UCD KAP1 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-08-23 2011-05-23 wgEncodeEH001764 1764 GSM935464 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Kap1UcdSig None Signal KRAB Associated Protein 1, helps regulate transcriptional repression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 KAP1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562JundIggrabSig K562 JunD IgR JunD K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002164 2164 GSM935569 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562JundIggrabSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 JunD IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifng6hStdSig K562 IFg6 IRF1 Sd IRF1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001866 1866 GSM935549 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Irf1Ifng6hStdSig IFNg6h Signal Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 6 hours (Snyder) Signal K562 IRF1 Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifng30StdSig K562 IFg3 IRF1 Sd IRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002799 2799 GSM935505 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Irf1Ifng30StdSig IFNg30 Signal Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Signal K562 IRF1 Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifna6hStdSig K562 IFa6 IRF1 Sd IRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002798 2798 GSM935504 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Irf1Ifna6hStdSig IFNa6h Signal Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon alpha treatment - 6 hours (Snyder) Signal K562 IRF1 Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifna30StdSig K562 IFa3 IRF1 Sd IRF1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001865 1865 GSM935546 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Irf1Ifna30StdSig IFNa30 Signal Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University 30 m of Interferon alpha (Snyder) Signal K562 IRF1 Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ini1IggmusSig K562 INI1 IgM Ini1 K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000725 725 GSM935634 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Ini1IggmusSig None Signal Ini1 (BAF47, SMARCB1) is a ubiquitous 47 kD component of the SWI/SNF chromatin-remodeling complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 INI1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Hmgn3StdSig K562 HMGN Std HMGN3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001863 1863 GSM935544 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Hmgn3StdSig None Signal HMGN3 is a high-mobility group protein. These proteins are small, 8 to 11 kDa, ubiquitous proteins believed to play a role in chromatin structure. HMGNs bind to nucleosomes between the histone core and DNA and reduce chromatin compaction. As a result HMGNs, HMGN3 included, are believed to increase access to DNA for DNA replication, repair and transcription. HMGN3 has specifically been implicated in the action of Thyroid horomone receptors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 HMGN3 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Hcfc1nb10068209IggrabSig K562 HCFC1 IgR HCFC1_(NB100-68209) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003392 3392 GSM1003625 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Hcfc1nb10068209IggrabSig None Signal The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 HCFC1 (NB100-68209) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gtf2f1ab28179IggrabSig K562 GT2F IgR GTF2F1_(AB28179) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001823 1823 GSM935501 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Gtf2f1ab28179IggrabSig None Signal RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 GTF2F1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gtf2bStdSig K562 GT2B Std GTF2B K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-06-14 2010-12-06 2011-09-06 wgEncodeEH000703 703 GSM935394 Snyder Harvard PeakSeq1.0 hg18 exp wgEncodeSydhTfbsK562Gtf2bStdSig None Signal DNA- binding general transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 GTF2B Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gata2UcdSig K562 GAT2 UCD GATA-2 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000683 683 GSM935373 Snyder USC hg18 exp wgEncodeSydhTfbsK562Gata2UcdSig None Signal GATA binding protein 2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 GATA2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gata1bIggmusSig K562 GATA1 IgM GATA1_(SC-266) K562 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003368 3368 GSM1003608 Snyder Stanford exp wgEncodeSydhTfbsK562Gata1bIggmusSig None Signal GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 GATA1 (SC-266) IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gata1UcdSig K562 GAT1 UCD GATA-1 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000638 638 GSM935540 Snyder USC hg18 exp wgEncodeSydhTfbsK562Gata1UcdSig None Signal GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 GATA1 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Elk112771IggrabSig K562 ELK1 IgR ELK1_(1277-1) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-03-01 2012-12-01 wgEncodeEH003356 3356 GSM1003620 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Elk112771IggrabSig None Signal Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 ELK1 (1277-1) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562E2f6UcdSig K562 E2F6 UCD E2F6 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000676 676 GSM935597 Snyder USC hg18 exp wgEncodeSydhTfbsK562E2f6UcdSig None Signal This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 E2F6 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562E2f4UcdSig K562 E2F4 UCD E2F4 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000671 671 GSM935600 Snyder USC hg18 exp wgEncodeSydhTfbsK562E2f4UcdSig None Signal mapping at the C-terminus of E2F4 of human origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal K562 E2F4 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CtcfbIggrabSig K562 CTCF IgR CTCF_(SC-15914) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002797 2797 GSM935407 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562CtcfbIggrabSig None Signal Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 CTCF IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Corestsc30189IggrabSig K562 COREST IgR COREST_(sc-30189) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-01-22 2012-10-21 wgEncodeEH002814 2814 GSM935439 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Corestsc30189IggrabSig None Signal Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 COREST SC30189 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Corestab24166IggrabSig K562 COREST IgR COREST_(ab24166) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002847 2847 GSM935385 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Corestab24166IggrabSig None Signal Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 COREST AB24166 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycStdSig K562 cMyc Std c-Myc K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000621 621 GSM935410 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycStdSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 c-Myc Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfng6hStdSig K562 IFg6 cMyc Sd c-Myc K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-04-08 wgEncodeEH000670 670 GSM935599 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycIfng6hStdSig IFNg6h Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Signal K562 c-Myc Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfng30StdSig K562 IFg3 cMyc Sd c-Myc K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-17 2011-05-17 wgEncodeEH001867 1867 GSM935548 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562CmycIfng30StdSig IFNg30 Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Signal K562 c-Myc Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfna6hStdSig K562 IFa6 cMyc Sd c-Myc K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000669 669 GSM935466 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycIfna6hStdSig IFNa6h Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Signal K562 c-Myc Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfna30StdSig K562 IFa3 cMyc Sd c-Myc K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000659 659 GSM935428 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycIfna30StdSig IFNa30 Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Signal K562 c-Myc Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIggrabSig K562 cMyc IgR c-Myc K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002800 2800 GSM935516 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562CmycIggrabSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 c-Myc IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunStdSig K562 cJun Std c-Jun K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000620 620 GSM935411 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunStdSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 c-Jun Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfng6hStdSig K562 IFg6 cJun Sd c-Jun K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000668 668 GSM935467 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunIfng6hStdSig IFNg6h Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Signal K562 c-Jun Standard IFNg 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfng30StdSig K562 IFg3 cJun Sd c-Jun K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000673 673 GSM935602 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunIfng30StdSig IFNg30 Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Signal K562 c-Jun Standard IFNg 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfna6hStdSig K562 IFa6 cJun Sd c-Jun K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000667 667 GSM935468 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunIfna6hStdSig IFNa6h Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Signal K562 c-Jun Standard IFNa 6hrs ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfna30StdSig K562 IFa3 cJun Sd c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002805 2805 GSM935521 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562CjunIfna30StdSig IFNa30 Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University 30 m of Interferon alpha (Snyder) Signal K562 c-Jun Standard IFNa 30min ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIggrabSig K562 c-Jun IgR c-Jun K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003369 3369 GSM1003609 Snyder Stanford exp wgEncodeSydhTfbsK562CjunIggrabSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 c-Jun IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Chd2ab68301IggrabSig K562 CHD2 IgR CHD2_(AB68301) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001822 1822 GSM935502 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Chd2ab68301IggrabSig None Signal CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 CHD2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CfosStdSig K562 cFOS Std c-Fos K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000619 619 GSM935355 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CfosStdSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal K562 c-FOS Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CebpbIggrabSig K562 CBPB IgR CEBPB K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001821 1821 GSM935499 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562CebpbIggrabSig None Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 CEBPB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Cdpsc6327IggrabSig K562 CDP IgR CDP_(sc-6327) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003391 3391 GSM1003622 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Cdpsc6327IggrabSig None Signal CDP (for CCAAT displacement protein) was identified as a repressor for tran- scription of developmentally regulated genes. It is a homeodomain protein that appears to compete with transcriptional activating proteins for binding to the promoter regions of various genes. CDP contains three cut repeats which function as DNA binding domains. It has been demonstrated that cut repeat domains have the capacity to bind to DNA in conjunction with or independently of homeodomain DNA binding. CDP has been shown to be the DNA-binding subunit of the HiNF-D complex, which contains cyclin A, Cdc2 and an Rb-related protein in addition to CDP. Histone expression is required for the transition to S phase in the cell cycle. The HiNF-D complex regulates the transcription of Histone H4, H3 and H1 genes, allowing cells to progress from G1 to S phase. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 CDP (SC-6327) IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ccnt2StdSig K562 CNT2 Std CCNT2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001864 1864 GSM935547 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Ccnt2StdSig None Signal CycT2 is one of three cyclins that can form a heterodimer with cyclin-dependent kinase 9 (CDK9). The heterodimer is known as positive elongation factor b (P-TEFb) and is responsible for the phosphophorylation of Ser2 of the heptad repeat in the C-terminal domain of RNA polymerase II as well as the negative elongation factors DSIF (hSpt4/hSpt5) and NELF. Phosphorylation of RNA polymerase II and the negative elongation factors by P-TEFb promotes elongation. CycT2 contains a leucine rich domain capable of binding to the C-terminal domain of RNA polymerase II. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 CCNT2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Brg1IggmusSig K562 BRG1 IgM Brg1 K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000724 724 GSM935633 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Brg1IggmusSig None Signal Brg1 (SMARCA4) is an ATPase subunit of the SWI/SNF chromatin-remodeling complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 BRG1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Brf2StdSig K562 BRF2 Std BRF2 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000767 767 GSM935490 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Brf2StdSig None Signal Brf2 is a component of an alternate form of the RNA Polymerase III transcription factor TFIIIB. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 BRF2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Brf1StdSig K562 BRF1 Std BRF1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000679 679 GSM935595 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Brf1StdSig None Signal 'B-related factor 1', subunit of RNA polymerase III transcription initiation factor IIIB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 BRF1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Bhlhe40nb100IggrabSig K562 BHL4 IgR BHLHE40_(NB100-1800) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEH001857 1857 GSM935616 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Bhlhe40nb100IggrabSig None Signal This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 BHLHE40 NB100 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Bdp1StdSig K562 BDP1 Std BDP1 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000678 678 GSM935594 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Bdp1StdSig None Signal 'B double-prime 1', subunit of RNA polymerase III transcription initiation factor IIIB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 BDP1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Bach1sc14700IggrabSig K562 Bach1 IgR Bach1_(sc-14700) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002846 2846 GSM935576 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Bach1sc14700IggrabSig None Signal This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 Bach1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Atf3StdSig K562 ATF3 Std ATF3 K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000700 700 GSM935391 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Atf3StdSig None Signal Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 ATF3 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Atf106325StdSig K562 ATF1 Std ATF1_(06-325) K562 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH002865 2865 GSM935340 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsK562Atf106325StdSig None Signal ATF1 is a bZip transcription factor from the CREB family. ATF1 binds to both cAMP response elements (TGACGTCA). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal K562 ATF1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Arid3asc8821IggrabSig K562 ARI3 IgR ARID3A_(sc-8821) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002861 2861 GSM935336 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Arid3asc8821IggrabSig None Signal This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal K562 ARID3A SC8821 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescInputUcdSig H1ES Inpt UCD Input H1-hESC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001751 1751 GSM935353 Snyder USC PeakSeq1.0 hg19 input wgEncodeSydhTfbsH1hescInputUcdSig None Signal embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal H1-hESC Input UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescInputIggrabSig H1ES Inpt IgR Input H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001834 1834 GSM935381 Snyder Stanford PeakSeq1.0 hg19 input wgEncodeSydhTfbsH1hescInputIggrabSig None Signal embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescZnf274m01UcdSig H1ES ZNF274 UCD ZNF274_(M01) H1-hESC UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-06-06 2013-03-05 wgEncodeEH003357 3357 GSM1003619 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsH1hescZnf274m01UcdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor and interacts with the KAP1 corepressor complex. embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal H1-hESC ZNF274 (M01) UC Davis ChIP-seq Signal from ENCODE/USC Regulation 
wgEncodeSydhTfbsH1hescZnf143IggrabSig H1ES Z143 IgR Znf143_(16618-1-AP) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002802 2802 GSM935514 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescZnf143IggrabSig None Signal Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC Znf143 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescUsf2IggrabSig H1ES USF2 IgR USF2 H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001837 1837 GSM935380 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescUsf2IggrabSig None Signal Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC USF2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescTbpIggrabSig H1ES TBP IgR TBP H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001848 1848 GSM935303 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescTbpIggrabSig None Signal General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC TBP IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescSuz12UcdSig H1ES SZ12 UCD SUZ12 H1-hESC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001752 1752 GSM935352 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescSuz12UcdSig None Signal Suppressor of zeste 12 homolog, Polycomb group (PcG) protein, Component of the PRC2/EED-EZH2 complex embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal H1-hESC SUZ12 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescSin3anb6001263IggrabSig H1ES SIN3A IgR SIN3A_(NB600-1263) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002854 2854 GSM935289 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescSin3anb6001263IggrabSig None Signal Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid &amp; thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR). embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC SIN3A IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescRfx5200401194IggrabSig H1ES RFX5 IgR RFX5_(200-401-194) H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001835 1835 GSM935382 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescRfx5200401194IggrabSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC RFX5 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescRad21IggrabSig H1ES Rad2 IgR Rad21 H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001836 1836 GSM935379 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescRad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescNrf1IggrabSig H1ES Nrf1 IgR Nrf1 H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH001847 1847 GSM935308 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescNrf1IggrabSig None Signal NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC Nrf1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescMxi1IggrabSig H1ES Mxi1 IgR Mxi1_(AF4185) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002829 2829 GSM935293 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescMxi1IggrabSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC Mxi1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescMaxUcdSig H1ES Max UCD Max H1-hESC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001757 1757 GSM935348 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescMaxUcdSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal H1-hESC Max UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescMafkIggrabSig H1ES MafK IgR MafK_(ab50322) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002828 2828 GSM935292 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescMafkIggrabSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC MafK IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescJundIggrabSig H1ES JunD IgR JunD H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002023 2023 GSM935434 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescJundIggrabSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC JunD IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescGtf2f1IggrabSig H1ES GT2F IgR GTF2F1_(AB28179) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002843 2843 GSM935581 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescGtf2f1IggrabSig None Signal RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC GTF2F1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCtbp2UcdSig H1ES CBP2 UCD CtBP2 H1-hESC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001767 1767 GSM935463 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescCtbp2UcdSig None Signal C-terminal binding protein 2 embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal H1-hESC CtBP2 UC Davis ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCmycIggrabSig H1ES cMyc IgR c-Myc H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002795 2795 GSM935509 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescCmycIggrabSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC c-Myc IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCjunIggrabSig H1ES cJun IgR c-Jun H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-19 wgEncodeEH001854 1854 GSM935614 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescCjunIggrabSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC c-Jun IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescChd2IggrabSig H1ES CHD2 IgR CHD2_(AB68301) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002827 2827 GSM935297 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescChd2IggrabSig None Signal CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC CHD2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescChd1a301218aIggrabSig H1ES CHD1 IgR CHD1_(A301-218A) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002826 2826 GSM935296 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescChd1a301218aIggrabSig None Signal CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC CHD1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCebpbIggrabSig H1ES CBPB IgR CEBPB H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002825 2825 GSM935295 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescCebpbIggrabSig None Signal Epitope mapping at the C-terminus of C/EBP-beta of rat origin embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC CEBPB IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescBrca1IggrabSig H1ES BRC1 IgR BRCA1_(A300-000A) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002801 2801 GSM935517 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescBrca1IggrabSig None Signal Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC BRCA1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescBach1sc14700IggrabSig H1ES Bach1 IgR Bach1_(sc-14700) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002842 2842 GSM935580 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescBach1sc14700IggrabSig None Signal This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. (provided by RefSeq) embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal H1-hESC Bach1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878InputStdSig GM78 Inpt Std Input GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000625 625 GSM935413 Snyder Yale hg18 input wgEncodeSydhTfbsGm12878InputStdSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal GM12878 Input Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878InputIggrabSig GM78 Inpt IgR Input GM12878 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-07-27 2012-04-27 wgEncodeEH000771 771 GSM935450 Snyder Stanford PeakSeq1.0 hg18 input wgEncodeSydhTfbsGm12878InputIggrabSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Input IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878InputTnfaIggrabSig GM78 TNF Inpt IgR Input GM12878 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH002034 2034 GSM935564 Snyder Stanford hg18 input wgEncodeSydhTfbsGm12878InputTnfaIggrabSig TNFa Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM12878 Input IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878InputIggmusSig GM78 Inpt IgM Input GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000706 706 GSM935390 Snyder Stanford hg18 input wgEncodeSydhTfbsGm12878InputIggmusSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Input IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Zzz3StdSig GM78 ZZZ3 Std ZZZ3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000698 698 GSM935483 Snyder Harvard hg18 exp wgEncodeSydhTfbsGm12878Zzz3StdSig None Signal ZZZ3 contains one ZZ-type zinc finger domain. ZZ type finger domains are named because of their ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions -they are most likely involved in ligand binding or molecular scaffolding. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal GM12878 ZZZ3 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Znf384hpa004051IggmusSig GM78 ZNF384 IgM ZNF384_(HPA004051) GM12878 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003388 3388 GSM1003602 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Znf384hpa004051IggmusSig None Signal This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 ZNF384 (HPA004051) IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Znf274StdSig GM78 Z274 Std ZNF274 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH001756 1756 GSM935349 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Znf274StdSig None Signal ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal GM12878 ZNF274 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Znf143166181apStdSig GM78 Z143 Std Znf143_(16618-1-AP) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001853 1853 GSM935613 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Znf143166181apStdSig None Signal Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Znf143 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Yy1StdSig GM78 YY1 Std YY1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000695 695 GSM935482 Snyder USC hg18 exp wgEncodeSydhTfbsGm12878Yy1StdSig None Signal YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal GM12878 YY1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878WhipIggmusSig GM78 WHIP IgM WHIP GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2010-04-26 2011-01-26 wgEncodeEH001787 1787 GSM935492 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878WhipIggmusSig None Signal Interacts with the N-terminal portion of Werner protein containing the exonuclease domain, shows homology to replication factor C family proteins, and is conserved from E. coli to human. Studies in yeast suggest that this gene may influence the aging process. Functions as a modulator for initiation or reinitiation events during DNA polymerase delta-mediated DNA synthesis. Has an intrinsic ATPase activity that functions as a sensor of DNA damage or of arrested replication forks and regulates the extent of DNA synthesis. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 WHIP IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Usf2IggmusSig GM78 USF2 IgM USF2 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001812 1812 GSM935558 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Usf2IggmusSig None Signal Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 USF2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Tr4StdSig GM78 TR4 Std TR4 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000697 697 GSM935480 Snyder USC hg18 exp wgEncodeSydhTfbsGm12878Tr4StdSig None Signal (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal GM12878 TR4 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878TbpIggmusSig GM78 TBP IgM TBP GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-06 2011-09-06 wgEncodeEH001798 1798 GSM935277 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878TbpIggmusSig None Signal General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 TBP IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusSig GM78 TBLR1 IgM TBLR1_(ab24550) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002853 2853 GSM935653 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusSig None Signal F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 TBLR1 AB24550 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Stat3IggmusSig GM78 STA3 IgM STAT3 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001811 1811 GSM935557 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Stat3IggmusSig None Signal Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 STAT3 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Stat1StdSig GM78 STA1 Std STAT1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001852 1852 GSM935612 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Stat1StdSig None Signal transcription factor, activated by interferon signalling B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 STAT1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Srebp2IggrabSig GM78 SREBP2 IgR SREBP2 GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003363 3363 GSM1003603 Snyder Stanford exp wgEncodeSydhTfbsGm12878Srebp2IggrabSig None Signal Sterol regulatory element binding transcription factor 2 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 SREBP2 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Srebp1IggrabSig GM78 SREBP1 IgR SREBP1 GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003362 3362 GSM1003617 Snyder Stanford exp wgEncodeSydhTfbsGm12878Srebp1IggrabSig None Signal Sterol regulatory element binding transcription factor 1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 SREBP1 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Spt20StdSig GM78 SPT Std SPT20 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001873 1873 GSM935417 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Spt20StdSig None Signal Also known as FAM48A or P38IP. It is a component of SAGA complex. Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down-regulation of E-cadherin during gastrulation by regulating E-cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by Fgf signaling and Snail. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal GM12878 SPT20 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Smc3ab9263IggmusSig GM78 SMC3 IgM SMC3_(ab9263) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001833 1833 GSM935376 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Smc3ab9263IggmusSig None Signal Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 SMC3 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Sin3anb6001263IggmusSig GM78 SIN3A IgM SIN3A_(NB600-1263) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEH002868 2868 GSM935331 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Sin3anb6001263IggmusSig None Signal Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid &amp; thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 SIN3A IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Rfx5200401194IggmusSig GM78 RFX5 IgM RFX5_(200-401-194) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001810 1810 GSM935556 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Rfx5200401194IggmusSig None Signal Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 RFX5 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Rad21IggrabSig GM78 Rad2 IgR Rad21 GM12878 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000749 749 GSM935332 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12878Rad21IggrabSig None Signal Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Rad21 IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol3StdSig GM78 Pol3 Std Pol3 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000645 645 GSM935316 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878Pol3StdSig None Signal RNA Polymerase III B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal GM12878 POL3 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol2s2IggmusSig GM78 PolS IgM Pol2(phosphoS2) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001858 1858 GSM935608 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Pol2s2IggmusSig None Signal RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Pol2 S2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol2StdSig GM78 Pol2 Std Pol2 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000626 626 GSM935412 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878Pol2StdSig None Signal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal GM12878 Pol2 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol2IggmusSig GM78 Pol2 IgM Pol2 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000708 708 GSM935386 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12878Pol2IggmusSig None Signal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Pol2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878P300bStdSig GM78 p300 Std p300_(SC-584) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002037 2037 GSM935562 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878P300bStdSig None Signal Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 p300 SC584 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878P300sc584IggmusSig GM78 p300 IgM p300_(SC-584) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001813 1813 GSM935559 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878P300sc584IggmusSig None Signal Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 p300 SC584 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878P300IggmusSig GM78 p300 IgM p300 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002824 2824 GSM935294 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878P300IggmusSig None Signal EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 p300 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Nrf1IggmusSig GM78 Nrf1 IgM Nrf1 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001846 1846 GSM935309 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Nrf1IggmusSig None Signal NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Nrf1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878NfybIggmusSig GM78 NYB IgM NF-YB GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002065 2065 GSM935507 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878NfybIggmusSig None Signal NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal GM12878 NF-YB IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878NfyaIggmusSig GM78 NYA IgM NF-YA GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002064 2064 GSM935506 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878NfyaIggmusSig None Signal NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal GM12878 NF-YA IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878NfkbTnfaIggrabSig GM78 TNF NKB IgR NFKB GM12878 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000690 690 GSM935478 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12878NfkbTnfaIggrabSig TNFa Signal Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Signal GM12878 NFKB IgG-rab TNFa ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Nfe2sc22827StdSig GM78 NFE2 Std NF-E2_(SC-22827) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-09-03 2011-06-03 wgEncodeEH001808 1808 GSM935652 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Nfe2sc22827StdSig None Signal Transcription factor NFE2 45 kDa subunit is a component of the NFE2 complex and essential for regulating erythroid and megakaryocytic maturation and differentiation. Binds to the hypersensitive site 2 (HS2) of the beta-globin control region (LCR). This subunit (NFE2)recognizes the TCAT/C sequence of the AP-1-like core palindrome present in a number of erythroid and megakaryocytic gene promoters. Requires MAFK or other small MAF proteins for binding to the NFE2 motif. May play a role in all aspects of hemoglobin production from globin and heme synthesis to procurement of iron. NFE2 has been shown to interact with CREB binding protein. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 NF-E2 SC22827 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Mxi1IggmusSig GM78 Mxi1 IgM Mxi1_(AF4185) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002026 2026 GSM935431 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Mxi1IggmusSig None Signal Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Mxi1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Mazab85725IggmusSig GM78 MAZ IgM MAZ_(ab85725) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002852 2852 GSM935283 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Mazab85725IggmusSig None Signal May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 MAZ IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878MaxIggmusSig GM78 Max IgM Max GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002806 2806 GSM935518 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878MaxIggmusSig None Signal The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 Max IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878MafkIggmusSig GM78 MafK IgM MafK_(ab50322) GM12878 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003361 3361 GSM1003616 Snyder Stanford exp wgEncodeSydhTfbsGm12878MafkIggmusSig None Signal NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 MafK (ab50322) IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878JundStdSig GM78 JunD Std JunD GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000639 639 GSM935541 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878JundStdSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal GM12878 JunD Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878JundIggrabSig GM78 JunD IgR JunD GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003370 3370 GSM1003634 Snyder Stanford exp wgEncodeSydhTfbsGm12878JundIggrabSig None Signal The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 JunD IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Irf3IggmusSig GM78 IRF3 IgM IRF3 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001809 1809 GSM935651 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Irf3IggmusSig None Signal Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 IRF3 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Ikzf1iknuclaStdSig GM78 IKZF1 Std IKZF1_(IkN)_(UCLA) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002811 2811 GSM935442 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Ikzf1iknuclaStdSig None Signal IKAROS family zinc finger 1 (Ikaros or IKZF1) is a C2H2 zinc finger transcription factor that is associated with various chromatin-modifying complexes and is suggested to play a role in the development of lymphocytes, B- and T-cells. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Signal GM12878 IKZF1 IKN UCLA Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Gcn5StdSig GM78 GCN5 Std GCN5 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-20 wgEncodeEH001874 1874 GSM935415 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Gcn5StdSig None Signal KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Signal GM12878 GCN5 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878ErraIggrabSig GM78 ERRA IgR ERRA GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003387 3387 GSM1003605 Snyder Stanford exp wgEncodeSydhTfbsGm12878ErraIggrabSig None Signal Epitope corresponding to amino acids 81-160 mapping near the N-terminus of ERRalpha of human origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 ERRA IgG-rab ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Elk112771IggmusSig GM78 ELK1 IgM ELK1_(1277-1) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002851 2851 GSM935345 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Elk112771IggmusSig None Signal Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 ELK1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Ebf1sc137065StdSig GM78 EBF1 Std EBF1_(SC-137065) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001832 1832 GSM935375 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Ebf1sc137065StdSig None Signal Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 EBF1 Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878E2f4IggmusSig GM78 E2F4 IgM E2F4 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEH002867 2867 GSM935330 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878E2f4IggmusSig None Signal mapping at the C-terminus of E2F4 of human origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 E2F4 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdSig GM78 CTCF Std CTCF_(SC-15914) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-19 wgEncodeEH001851 1851 GSM935611 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdSig None Signal Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 CTCF Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Corestsc30189IggmusSig GM78 COREST IgM COREST_(sc-30189) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002841 2841 GSM935583 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Corestsc30189IggmusSig None Signal Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 COREST SC30189 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Chd2ab68301IggmusSig GM78 CHD2 IgM CHD2_(AB68301) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001831 1831 GSM935378 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Chd2ab68301IggmusSig None Signal CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 CHD2 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Chd1a301218aIggmusSig GM78 CHD1 IgM CHD1_(A301-218A) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002823 2823 GSM935301 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Chd1a301218aIggmusSig None Signal CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 CHD1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878CfosStdSig GM78 cFOS Std c-Fos GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-12-02 2011-09-01 wgEncodeEH000622 622 GSM935409 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878CfosStdSig None Signal Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Signal GM12878 c-FOS Standard ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Cdpsc6327IggmusSig GM78 CDP IgM CDP_(sc-6327) GM12878 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003386 3386 GSM1003604 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Cdpsc6327IggmusSig None Signal CDP (for CCAAT displacement protein) was identified as a repressor for tran- scription of developmentally regulated genes. It is a homeodomain protein that appears to compete with transcriptional activating proteins for binding to the promoter regions of various genes. CDP contains three cut repeats which function as DNA binding domains. It has been demonstrated that cut repeat domains have the capacity to bind to DNA in conjunction with or independently of homeodomain DNA binding. CDP has been shown to be the DNA-binding subunit of the HiNF-D complex, which contains cyclin A, Cdc2 and an Rb-related protein in addition to CDP. Histone expression is required for the transition to S phase in the cell cycle. The HiNF-D complex regulates the transcription of Histone H4, H3 and H1 genes, allowing cells to progress from G1 to S phase. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 CDP (SC-6327) IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Brca1a300IggmusSig GM78 BRC1 IgM BRCA1_(A300-000A) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001830 1830 GSM935377 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Brca1a300IggmusSig None Signal Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 BRCA1 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Bhlhe40cIggmusSig GM78 BHL4 IgM BHLHE40_(NB100-1800) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002025 2025 GSM935430 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Bhlhe40cIggmusSig None Signal This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Signal GM12878 BHLHE40 NB100 IgG-mus ChIP-seq Signal from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsViewPeaks Peaks Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard Regulation 
wgEncodeSydhTfbsU2osSetdb1UcdPk U2OS STDB UCD SETDB1 U2OS UCDavis ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001762 1762 GSM935458 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsU2osSetdb1UcdPk None Peaks SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment U2OS SETDB1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsU2osKap1UcdPk U2OS KAP1 UCD KAP1 U2OS UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-05-31 wgEncodeEH001776 1776 GSM935587 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsU2osKap1UcdPk None Peaks KRAB Associated Protein 1, helps regulate transcriptional repression. osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment U2OS KAP1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsShsy5yGata3sc269sc269UcdPk SHSY GAT3 UCD GATA3_(SC-269) SH-SY5Y UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002031 2031 GSM935567 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsShsy5yGata3sc269sc269UcdPk None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq) neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment SH-SY5Y GATA3 SC269 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsShsy5yGata2UcdPk SHSY GAT2 UCD GATA-2 SH-SY5Y UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001770 1770 GSM935589 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsShsy5yGata2UcdPk None Peaks GATA binding protein 2 neuroblastoma clonal subline of the neuroepithelioma cell line SK-N-SH from the 1970 bone marrow biopsy of a 4-year-old girl with metastatic neuroblastoma, trisomy of 1q Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment SH-SY5Y GATA2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsRajiPol2UcdPk Raji Pol2 UCD Pol2 Raji UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH001761 1761 GSM935461 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsRajiPol2UcdPk None Peaks RNA Polymerase II B lymphocyte, "The Raji line of lymphoblast-like cells was established by R.J.V. Pulvertaft in 1963 from a Burkitt's lymphoma of the left maxilla of an 11-year-old Black male." - ATCC. (PMID: 14086209) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment Raji Pol2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdefetalGata1UcdPk PBDF GAT1 UCD GATA-1 PBDEFetal UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-05-13 2012-02-13 wgEncodeEH001785 1785 GSM935333 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPbdefetalGata1UcdPk None Peaks GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. peripheral blood-derived erythroblasts from 16-19 week human fetal liver Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBDE-Fetal GATA1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdePol2UcdPk PBDE Pol2 UCD Pol2 PBDE UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-10-13 2011-07-13 wgEncodeEH001766 1766 GSM935462 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPbdePol2UcdPk None Peaks RNA Polymerase II peripheral blood-derived erythroblasts Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBDE Pol2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPbdeGata1UcdPk PBDE GAT1 UCD GATA-1 PBDE UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-09-23 2011-06-23 wgEncodeEH001765 1765 GSM935465 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPbdeGata1UcdPk None Peaks GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. peripheral blood-derived erythroblasts Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PBDE GATA1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsPanc1Tcf7l2UcdPk PANC TCF7L2 UCD TCF7L2 PANC-1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002071 2071 GSM816437 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsPanc1Tcf7l2UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment PANC1 TCF7L2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1Znf274UcdPk NT2D Z274 UCD ZNF274 NT2-D1 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001775 1775 GSM935584 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsNt2d1Znf274UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2-D1 ZNF274 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1Yy1UcdPk NT2D YY1 UCD YY1 NT2-D1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000653 653 GSM935424 Snyder USC hg18 exp wgEncodeSydhTfbsNt2d1Yy1UcdPk None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2-D1 YY1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNt2d1Suz12UcdPk NT2D SZ12 UCD SUZ12 NT2-D1 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000652 652 GSM935423 Snyder USC hg18 exp wgEncodeSydhTfbsNt2d1Suz12UcdPk None Peaks Suppressor of zeste 12 homolog, Polycomb group (PcG) protein, Component of the PRC2/EED-EZH2 complex malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment NT2-D1 SUZ12 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4Pol2StdPk NB4 Pol2 Std Pol2 NB4 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000618 618 GSM935354 Snyder Yale hg18 exp wgEncodeSydhTfbsNb4Pol2StdPk None Peaks RNA Polymerase II acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment NB4 Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4MaxStdPk NB4 Max Std Max NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-26 2011-05-26 wgEncodeEH001806 1806 GSM935644 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsNb4MaxStdPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment NB4 Max Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsNb4CmycStdPk NB4 cMyc Std c-Myc NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-26 2011-05-26 wgEncodeEH001807 1807 GSM935643 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsNb4CmycStdPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment NB4 c-Myc Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesStat3TamStdPk MCF1 TAM STA3 Std STAT3 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001769 1769 GSM935457 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesStat3TamStdPk 4OHTAM_1uM_36hr Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Regions of enriched signal in experiment MCF10A STAT3 Standard 4-hydroxytamoxifen 36hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesStat3Etoh01StdPk MCF1 EtH STA3 Std STAT3 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001772 1772 GSM935591 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesStat3Etoh01StdPk EtOH_0.01pct Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10A STAT3 Standard EtOH .01% 36h ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesStat3Tam112hHvdPk MCF1 TAM 12h STA3 STAT3 MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002836 2836 GSM935399 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesStat3Tam112hHvdPk 4OHTAM_1uM_12hr Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Regions of enriched signal in experiment MCF10A STAT3 Harvard 4-hydroxytamoxifen 12hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesPol2TamStdPk MCF1 TAM Pol2 Std Pol2 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001768 1768 GSM935456 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesPol2TamStdPk 4OHTAM_1uM_36hr Peaks RNA Polymerase II mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Regions of enriched signal in experiment MCF10A Pol2 Standard 4-hydroxytamoxifen 36hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesPol2Etoh01StdPk MCF1 EtH Pol2 Std Pol2 MCF10A-Er-Src std ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001771 1771 GSM935588 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf10aesPol2Etoh01StdPk EtOH_0.01pct Peaks RNA Polymerase II mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10A Pol2 Standard EtOH .01% 36h ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesE2f4TamHvdPk MCF1 TAM E2F4 Hvd E2F4 MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002835 2835 GSM935400 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesE2f4TamHvdPk 4OHTAM_1uM_36hr Peaks mapping at the C-terminus of E2F4 of human origin mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Regions of enriched signal in experiment MCF10A E2F4 Harvard 4-hydroxytamoxifen 36hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCmycTam14hHvdPk MCF1 TAM 14h cMyc c-Myc MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002840 2840 GSM935491 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCmycTam14hHvdPk 4OHTAM_1uM_4hr Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Regions of enriched signal in experiment MCF10A c-Myc Harvard 4-hydroxytamoxifen 14hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCmycEtoh01HvdPk MCF1 EtH cMyc Hvd c-Myc MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002816 2816 GSM935441 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCmycEtoh01HvdPk EtOH_0.01pct Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10A c-Myc Harvard EtOH .01% 36h ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosTam14hHvdPk MCF1 TAM 14h cFOS c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002838 2838 GSM935397 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosTam14hHvdPk 4OHTAM_1uM_4hr Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 4 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Regions of enriched signal in experiment MCF10A c-FOS Harvard 4-hydroxytamoxifen 14hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosTam112hHvdPk MCF1 TAM 12h cFOS c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002837 2837 GSM935398 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosTam112hHvdPk 4OHTAM_1uM_12hr Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 12 hours with 1 uM 4-hydroxytamoxifen dissolved in ethanol (Struhl) Regions of enriched signal in experiment MCF10A c-FOS Harvard 4-hydroxytamoxifen 12hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosTamHvdPk MCF1 TAM cFOS Hvd c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-07 2012-11-07 wgEncodeEH002839 2839 GSM935396 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosTamHvdPk 4OHTAM_1uM_36hr Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers) Regions of enriched signal in experiment MCF10A c-FOS Harvard 4-hydroxytamoxifen 36hr ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf10aesCfosEtoh01HvdPk MCF1 EtH cFOS Hvd c-Fos MCF10A-Er-Src Harvard_Control ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002815 2815 GSM935438 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsMcf10aesCfosEtoh01HvdPk EtOH_0.01pct Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER) input library was prepared at Harvard. Chromatin IP Sequencing Snyder Struhl - Harvard University 36 h with 0.01% Ethanol (Snyder) Regions of enriched signal in experiment MCF10A c-FOS Harvard EtOH .01% 36h ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293tZnf263UcdPk HEKT Z263 UCD ZNF263 HEK293-T-REx UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-24 2011-10-24 wgEncodeEH001781 1781 GSM935577 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293tZnf263UcdPk None Peaks ZNF263 (NP_005732, 201 a.a. ~ 299 a.a) partial recombinant protein with GST tag. embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line, hypotriploid, XXX Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEK293-T-REx ZNF263 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Tcf7l2UcdPk HEK2 TCF7L2 UCD TCF7L2 HEK293 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-22 2012-03-22 wgEncodeEH002022 2022 GSM782124 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293Tcf7l2UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEK293 TCF7L2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Pol2StdPk HEK2 Pol2 Std Pol2 HEK293 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000632 632 GSM935534 Snyder Yale hg18 exp wgEncodeSydhTfbsHek293Pol2StdPk None Peaks RNA Polymerase II embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment HEK293 Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Kap1UcdPk HEK2 KAP1 UCD KAP1 HEK293 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-05-31 wgEncodeEH001779 1779 GSM935592 Snyder USC PeakSeq1.0. KAP1 colocalizes with H3K9me3 marks and peak analysis should be performed using programs modified for spreading histone marks such as H3K9me3 and H3K27me3. hg19 exp wgEncodeSydhTfbsHek293Kap1UcdPk None Peaks KRAB Associated Protein 1, helps regulate transcriptional repression. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEK293 KAP1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHek293Elk4UcdPk HEK2 ELK4 UCD ELK4 HEK293 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-05-31 wgEncodeEH001773 1773 GSM935590 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHek293Elk4UcdPk None Peaks This gene is a member of the Ets family of transcription factors and of the ternary complex factor (TCF) subfamily. (provided by RefSeq) embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEK293 ELK4 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHct116Tcf7l2UcdPk HCT TCF7L2 UCD TCF7L2 HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000629 629 GSM782123 Snyder USC hg18 exp wgEncodeSydhTfbsHct116Tcf7l2UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HCT-116 TCF7L2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHct116Pol2UcdPk HCT Pol2 UCD Pol2 HCT-116 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000651 651 GSM935426 Snyder USC hg18 exp wgEncodeSydhTfbsHct116Pol2UcdPk None Peaks RNA Polymerase II colorectal carcinoma (PMID: 7214343) Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HCT-116 Pol2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19193Pol2IggmusPk GM93 Pol2 IgM Pol2 GM19193 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000743 743 GSM935325 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19193Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM19193 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19193NfkbTnfaIggrabPk GM93 TNF NKB IgR NFKB GM19193 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000718 718 GSM935279 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19193NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM19193 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19099Pol2IggmusPk GM99 Pol2 IgM Pol2 GM19099 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000741 741 GSM935323 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19099Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM19099 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm19099NfkbTnfaIggrabPk GM99 TNF NKB IgR NFKB GM19099 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000717 717 GSM935273 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm19099NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM19099 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18951Pol2IggmusPk GM51 Pol2 IgM Pol2 GM18951 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000739 739 GSM935530 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18951Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM18951 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18951NfkbTnfaIggrabPk GM51 TNF NKB IgR NFKB GM18951 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000738 738 GSM935531 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18951NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Japanese in Tokyo, Japan, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM18951 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18526Pol2IggmusPk GM26 Pol2 IgM Pol2 GM18526 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000733 733 GSM935524 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18526Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM18526 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18526NfkbTnfaIggrabPk GM26 TNF NKB IgR NFKB GM18526 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000716 716 GSM935281 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18526NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Han Chinese in Beijing, China, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM18526 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18505Pol2IggmusPk GM05 Pol2 IgM Pol2 GM18505 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2012-03-09 wgEncodeEH000731 731 GSM935522 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18505Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM18505 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm18505NfkbTnfaIggrabPk GM05 TNF NKB IgR NFKB GM18505 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000715 715 GSM935282 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm18505NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM18505 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm15510Pol2IggmusPk GM10 Pol2 IgM Pol2 GM15510 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000714 714 GSM935291 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm15510Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM15510 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm15510NfkbTnfaIggrabPk GM10 TNF NKB IgR NFKB GM15510 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000736 736 GSM935529 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm15510NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid NIGMS Human Genetic Cell Repository, DNA Polymorphism Discovery Resource Collection, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM15510 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12892Pol2IggmusPk GM92 Pol2 IgM Pol2 GM12892 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000729 729 GSM935640 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12892Pol2IggmusPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12892 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12892NfkbTnfaIggrabPk GM92 TNF NKB IgR NFKB GM12892 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000712 712 GSM935285 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12892NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM12892 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12891Pol2IggmusPk GM91 Pol2 IgM Pol2 GM12891 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000710 710 GSM935287 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12891Pol2IggmusPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12891 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12891NfkbTnfaIggrabPk GM91 TNF NKB IgR NFKB GM12891 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000735 735 GSM935526 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12891NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM12891 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm10847Pol2IggmusPk GM47 Pol2 IgM Pol2 GM10847 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2012-03-09 wgEncodeEH000705 705 GSM935389 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm10847Pol2IggmusPk None Peaks RNA Polymerase II lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM10847 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm10847NfkbTnfaIggrabPk GM47 TNF NKB IgR NFKB GM10847 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000734 734 GSM935527 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm10847NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM10847 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm08714Znf274UcdPk GM14 Z274 UCD ZNF274 GM08714 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEH002866 2866 GSM935329 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsGm08714Znf274UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. lymphoblastoid cell line, Instability of heterochromatin of chromosomes 1, 9, and 16 with variable combined immunodeficiency; dysmorphic facial features, developmental delay, malabsorption, and recurrent infections; see GM08747 Fibroblast; donor subject is a compound heterozygote: one allele has a G&gt;A transition at nucleotide 1807 (1807G&gt;A) of the DNMT3B gene resulting in an Ala to Thr substitution at codon 603 [Ala603Thr (A603T)], the mutation occurring in a region between motifs I and IV within the catalytic domain of DNMT3B; the second allele has a G&gt;A transition within intron 22 located 11 nucleotides 5-prime of the normal splice acceptor site [IVS22AS,G&gt;A,-11] resulting in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA. This results in the insertion of 3 amino acids (serine, threonine, and proline) at codon 744 (744ins3). The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo. Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment GM08714 ZNF274 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshSmc3IggrabPk SKSH SMC3 IgR SMC3_(ab9263) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003377 3377 GSM1003627 Snyder Stanford exp wgEncodeSydhTfbsSknshSmc3IggrabPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH SMC3 (ab9263) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshRfx5IggrabPk SKSH RFX5 IgR RFX5_(200-401-194) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003375 3375 GSM1003629 Snyder Stanford exp wgEncodeSydhTfbsSknshRfx5IggrabPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH RFX5 (200-401-194) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshRad21IggrabPk SKSH Rad21 IgR Rad21 SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003376 3376 GSM1003628 Snyder Stanford exp wgEncodeSydhTfbsSknshRad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshP300bIggrabPk SKSH p300 IgR p300_(SC-584) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003378 3378 GSM1003626 Snyder Stanford exp wgEncodeSydhTfbsSknshP300bIggrabPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH p300 (SC-584) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshNrf1IggrabPk SKSH Nrf1 IgR Nrf1 SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003374 3374 GSM1003630 Snyder Stanford exp wgEncodeSydhTfbsSknshNrf1IggrabPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH Nrf1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshMxi1IggrabPk SKSH Mxi1 IgR Mxi1_(AF4185) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003373 3373 GSM1003631 Snyder Stanford exp wgEncodeSydhTfbsSknshMxi1IggrabPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH Mxi1 (AF4185) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshJundIggrabPk SKSH JunD IgR JunD SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003372 3372 GSM1003632 Snyder Stanford exp wgEncodeSydhTfbsSknshJundIggrabPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH JunD IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsSknshCtcfbIggrabPk SKSH CTCF IgR CTCF_(SC-15914) SK-N-SH IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003371 3371 GSM1003633 Snyder Stanford exp wgEncodeSydhTfbsSknshCtcfbIggrabPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual. Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment SK-N-SH CTCF (SC-15914) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Znf217UcdPk MCF7 Z217 UCD ZNF217 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-08-03 2012-05-03 wgEncodeEH002036 2036 GSM935563 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf7Znf217UcdPk None Peaks ZNF217 is an important oncogene based on the high frequency of amplification and overexpression in many cancer types, but its molecular mode of gene regulation is poorly understood. ZNF217 has been purified in complexes that contain repressor proteins such as CtBP2, suggesting that it acts as a transcriptional repressor. ZNF217 contains seven C2H2 zinc finger domains and has been shown to bind to gene promoters mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 ZNF217 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Tcf7l2UcdPk MCF7 TCF7L2 UCD TCF7L2 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-20 2012-06-19 wgEncodeEH002072 2072 GSM816438 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf7Tcf7l2UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 TCF7L2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Hae2f1UcdPk MCF7 HAE2 UCD HA-E2F1 MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000693 693 GSM935477 Snyder USC hg18 exp wgEncodeSydhTfbsMcf7Hae2f1UcdPk None Peaks The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 HA-E2F1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Gata3sc269UcdPk MCF7 GAT3 UCD GATA3_(SC-269) MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002812 2812 GSM935445 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsMcf7Gata3sc269UcdPk None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq) mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 GATA3 SC269 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsMcf7Gata3UcdPk MCF7 GAT3 UCD GATA3_(SC-268) MCF-7 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-08-03 2012-05-03 wgEncodeEH002035 2035 GSM825711 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsMcf7Gata3UcdPk None Peaks This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq). mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment MCF-7 GATA3 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Rfx5IggrabPk IMR90 RFX5 IgR RFX5_(200-401-194) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003367 3367 GSM1003615 Snyder Stanford exp wgEncodeSydhTfbsImr90Rfx5IggrabPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 RFX5 (200-401-194) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Rad21IggrabPk IMR90 Rad2 IgR Rad21 IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002810 2810 GSM935624 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90Rad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Pol2IggrabPk IMR90 Pol2 IgR Pol2 IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002809 2809 GSM935513 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90Pol2IggrabPk None Peaks RNA Polymerase II fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 Pol2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Mxi1IggrabPk IMR90 Mxi1 IgR Mxi1_(AF4185) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003366 3366 GSM1003614 Snyder Stanford exp wgEncodeSydhTfbsImr90Mxi1IggrabPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 Mxi1 (AF4185) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Mazab85725IggrabPk IMR90 MAZ IgR MAZ_(ab85725) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003365 3365 GSM1003613 Snyder Stanford exp wgEncodeSydhTfbsImr90Mazab85725IggrabPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 MAZ (ab85725) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90MafkIggrabPk IMR90 MafK IgR MafK_(ab50322) IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002832 2832 GSM935403 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90MafkIggrabPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 MafK IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90CtcfbIggrabPk IMR90 CTCF IgR CTCF_(SC-15914) IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002831 2831 GSM935404 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90CtcfbIggrabPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 CTCF IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Corestsc30189IggrabPk IMR90 COREST IgR COREST_(sc-30189) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003364 3364 GSM1003612 Snyder Stanford exp wgEncodeSydhTfbsImr90Corestsc30189IggrabPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 COREST (SC-30189) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90Chd1nb10060411IggrabPk IMR90 CHD1 IgR CHD1_(NB100-60411) IMR90 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003390 3390 GSM1003623 Snyder Stanford exp wgEncodeSydhTfbsImr90Chd1nb10060411IggrabPk None Peaks ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 CHD1 (NB100-60411) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsImr90CebpbIggrabPk IMR90 CBPB IgR CEBPB IMR90 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002807 2807 GSM935519 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsImr90CebpbIggrabPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin fetal lung fibroblasts, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment IMR90 CEBPB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecPol2StdPk HUVEC Pol2 Std Pol2 HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000702 702 GSM935393 Snyder Stanford hg18 exp wgEncodeSydhTfbsHuvecPol2StdPk None Peaks RNA Polymerase II umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HUVEC Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecMaxStdPk HUVEC Max Std Max HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000768 768 GSM935572 Snyder Stanford hg18 exp wgEncodeSydhTfbsHuvecMaxStdPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HUVEC Max Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecGata2UcdPk HUVEC GAT2 UCD GATA-2 HUVEC UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH001758 1758 GSM935347 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHuvecGata2UcdPk None Peaks GATA binding protein 2 umbilical vein endothelial cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HUVEC GATA2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecCjunStdPk HUVEC cJun Std c-Jun HUVEC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000719 719 GSM935278 Snyder Stanford hg18 exp wgEncodeSydhTfbsHuvecCjunStdPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HUVEC c-Jun Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHuvecCfosUcdPk HUVEC cFOS UCD c-Fos HUVEC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2011-01-13 2011-10-13 wgEncodeEH001774 1774 GSM935585 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHuvecCfosUcdPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. umbilical vein endothelial cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HUVEC c-FOS UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Znf274UcdPk HEPG Z274 UCD ZNF274 HepG2 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-10 2011-02-10 wgEncodeEH001755 1755 GSM935350 Snyder USC PeakSeq1.0.  Replicate overlap below cutoff, but submitted because there are very few biologically real targets and all the targets are in heterochromatic regions. hg19 exp wgEncodeSydhTfbsHepg2Znf274UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEPG2 ZNF274 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Usf2IggrabPk HEPG USF2 IgR USF2 HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001804 1804 GSM935646 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Usf2IggrabPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 USF2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Tr4UcdPk HEPG TR4 UCD TR4 HepG2 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000675 675 GSM935596 Snyder USC hg18 exp wgEncodeSydhTfbsHepg2Tr4UcdPk None Peaks (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEPG2 TR4 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Tcf7l2UcdPk HEPG TCF7L2 UCD TCF7L2 HepG2 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2001-06-27 2011-01-19 2011-10-19 wgEncodeEH001780 1780 GSM782122 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Tcf7l2UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 hepatocellular carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HEPG2 TCF7L2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2TbpIggrabPk HEPG TBP IgR TBP HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001793 1793 GSM935280 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2TbpIggrabPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 TBP IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Srebp2PravastStdPk HEPG prav SBP2 Sd SREBP2 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000643 643 GSM935314 Snyder Yale hg18 exp wgEncodeSydhTfbsHepg2Srebp2PravastStdPk pravastatin Peaks Sterol regulatory element binding transcription factor 2 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Regions of enriched signal in experiment HEPG2 SREBP2 Standard pravastatin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Srebp1PravastStdPk HEPG prav SRBP Sd SREBP1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000642 642 GSM935315 Snyder Yale hg18 exp wgEncodeSydhTfbsHepg2Srebp1PravastStdPk pravastatin Peaks Sterol regulatory element binding transcription factor 1 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Regions of enriched signal in experiment HEPG2 SREBP1 Standard pravastatin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Srebp1InslnStdPk HEPG isln SRBP Sd SREBP1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000759 759 GSM935627 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Srebp1InslnStdPk insulin Peaks Sterol regulatory element binding transcription factor 1 hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University DMEM with 0.5% BSA supplemented with 100 nM insulin and 10 uM 22-hydroxycholesterol for 6 h. (Snyder) Regions of enriched signal in experiment HEPG2 SREBP1 Standard insulin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Smc3ab9263IggrabPk HEPG SMC3 IgR SMC3_(ab9263) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001861 1861 GSM935542 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Smc3ab9263IggrabPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 SMC3 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Rfx5200401194IggrabPk HEPG RFX5 IgR RFX5_(200-401-194) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001843 1843 GSM935304 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Rfx5200401194IggrabPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 RFX5 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Rad21IggrabPk HEPG Rad2 IgR Rad21 HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001803 1803 GSM935647 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Rad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2s2IggrabPk HEPG PolS IgR Pol2(phosphoS2) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001860 1860 GSM935543 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Pol2s2IggrabPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 Pol2 S2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2PravastStdPk HEPG prav Pol2 Sd Pol2 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000641 641 GSM935312 Snyder Yale hg18 exp wgEncodeSydhTfbsHepg2Pol2PravastStdPk pravastatin Peaks RNA Polymerase II hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University For sterol deprivation, cells were cultured with pravastatin (2 uM, Sigma) in DMEM with 0.5% BSA for 16 h. (Snyder) Regions of enriched signal in experiment HEPG2 Pol2 Standard pravastatin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2ForsklnStdPk HEPG frsk Pol2 Sd Pol2 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000758 758 GSM935628 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Pol2ForsklnStdPk forskolin Peaks RNA Polymerase II hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 Pol2 Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pol2IggrabPk HEPG Pol2 IgR Pol2 HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001792 1792 GSM935603 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Pol2IggrabPk None Peaks RNA Polymerase II hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 Pol2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Pgc1aForsklnStdPk HEPG frsk PGC1 Sd PGC1A HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000757 757 GSM935623 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Pgc1aForsklnStdPk forskolin Peaks The protein encoded by this gene is a transcriptional coactivator that regulates the genes involved in energy metabolism. This protein interacts with PPARgamma, which permits the interaction of this protein with multiple transcription factors. This protein can interact with, and regulate the activities of, cAMP response element binding protein (CREB) and nuclear respiratory factors (NRFs). hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 PGC1A Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2P300sc582IggrabPk HEPG p300 IgR p300_(SC-584) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001862 1862 GSM935545 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2P300sc582IggrabPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 p300 SC584 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Nrf1IggrabPk HEPG Nrf1 IgR Nrf1 HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001802 1802 GSM935648 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Nrf1IggrabPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 Nrf1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mafksc477IggrabPk HEPG MafK IgR MafK_(SC-477) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH001850 1850 GSM935610 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Mafksc477IggrabPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 MafK SC477 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mxi1StdPk HEPG Mxi1 Std Mxi1_(AF4185) HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002029 2029 GSM935437 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Mxi1StdPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 Mxi1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mazab85725IggrabPk HEPG MAZ IgR MAZ_(ab85725) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002860 2860 GSM935335 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2Mazab85725IggrabPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 MAZ IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2MaxIggrabPk HEPG Max IgR Max HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002796 2796 GSM935406 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2MaxIggrabPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 Max IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Mafkab50322IggrabPk HEPG MafK IgR MafK_(ab50322) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001842 1842 GSM935305 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Mafkab50322IggrabPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 MafK IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Maffm8194IggrabPk HEPG MafF IgR MafF_(M8194) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001841 1841 GSM935306 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Maffm8194IggrabPk None Peaks The protein encoded by this gene is a (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. Can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. May also be involved in the cellular stress response. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 MafF IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2JundIggrabPk HEPG JunD IgR JunD HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001801 1801 GSM935649 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2JundIggrabPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 JunD IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Irf3IggrabPk HEPG IRF3 IgR IRF3 HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001800 1800 GSM935650 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Irf3IggrabPk None Peaks Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 IRF3 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Hsf1ForsklnStdPk HEPG frsk HSF1 Sd HSF1 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000754 754 GSM935626 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Hsf1ForsklnStdPk forskolin Peaks Epitope corresponding to amino acids 219-529 of heat shock transcription factor 1 (HSF1) of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 HSF1 Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Hnf4aForsklnStdPk HEPG frsk HNF4 Sd HNF4A HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000753 753 GSM935619 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Hnf4aForsklnStdPk forskolin Peaks Epitope mapping at the C-terminus of Rab 11 of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 HNF4A Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Grp20ForsklnStdPk HEPG frsk GR20 Sd GRp20 HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000752 752 GSM935620 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2Grp20ForsklnStdPk forskolin Peaks Epitope mapping at the C-terminus of GR alpha of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 GRp20 Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2ErraForsklnStdPk HEPG frsk ERRA Sd ERRA HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000751 751 GSM935621 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2ErraForsklnStdPk forskolin Peaks Epitope corresponding to amino acids 81-160 mapping near the N-terminus of ERRalpha of human origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 ERRA Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Corestsc30189IggrabPk HEPG COREST IgR COREST_(sc-30189) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002845 2845 GSM935579 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2Corestsc30189IggrabPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 COREST SC30189 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CjunIggrabPk HEPG cJun IgR c-Jun HepG2 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001794 1794 GSM935364 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2CjunIggrabPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 c-Jun IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Chd2ab68301IggrabPk HEPG CHD2 IgR CHD2_(AB68301) HepG2 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001840 1840 GSM935307 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Chd2ab68301IggrabPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 CHD2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CebpzIggrabPk HEPG CEBPZ IgR CEBPZ HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002859 2859 GSM935274 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2CebpzIggrabPk None Peaks Stimulates transcription from the HSP70 promoter. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 CEBPZ IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CebpbForsklnStdPk HEPG frsk CBPB Sd CEBPB HepG2 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000750 750 GSM935622 Snyder Stanford hg18 exp wgEncodeSydhTfbsHepg2CebpbForsklnStdPk forskolin Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University low-glucose DMEM with 0.5% BSA supplemented with 1uM forskolin and 1mM pyruvate for 6h. (Snyder) Regions of enriched signal in experiment HEPG2 CEBPB Standard forskolin ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2CebpbIggrabPk HEPG CBPB IgR CEBPB HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-04 2011-01-14 2011-10-13 wgEncodeEH001829 1829 GSM935493 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2CebpbIggrabPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 CEBPB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Brca1a300IggrabPk HEPG BRC1 IgR BRCA1_(A300-000A) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001859 1859 GSM935609 Snyder Stanford PeakSeq1.0.  Although this dataset narrowly misses the ENCODE standard for peak concordance, we submit this data because we feel it is of good quality and will be particularly valuable for comparison to BRCA1 datasets in other cell lines. hg19 exp wgEncodeSydhTfbsHepg2Brca1a300IggrabPk None Peaks Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 BRCA1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Bhlhe40cIggrabPk HEPG BHL4 IgR BHLHE40_(NB100-1800) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002032 2032 GSM935566 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHepg2Bhlhe40cIggrabPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 BHLHE40 NB100 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHepg2Arid3anb100279IggrabPk HEPG ARI3 IgR ARID3A_(NB100-279) HepG2 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002858 2858 GSM935275 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHepg2Arid3anb100279IggrabPk None Peaks This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. (provided by RefSeq) hepatocellular carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HEPG2 ARID3A NB100279 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Zzz3StdPk HeLa ZZZ3 Std ZZZ3 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-17 2011-05-17 wgEncodeEH001872 1872 GSM935416 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Zzz3StdPk None Peaks ZZZ3 contains one ZZ-type zinc finger domain. ZZ type finger domains are named because of their ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions -they are most likely involved in ligand binding or molecular scaffolding. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 ZZZ3 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Znf274UcdPk HeLa Z274 UCD ZNF274 HeLa-S3 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-08-17 2011-05-17 wgEncodeEH001763 1763 GSM935459 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Znf274UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 ZNF274 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Znf143IggrabPk HeLa Z143 IgR Znf143_(16618-1-AP) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002028 2028 GSM935436 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Znf143IggrabPk None Peaks Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 Znf143 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Zkscan1hpa006672IggrabPk HeLa ZKSCN1 IgR ZKSCAN1_(HPA006672) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002857 2857 GSM935362 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Zkscan1hpa006672IggrabPk None Peaks The ZKSCAN1 gene encodes a transcriptional regulator of the KRAB (Kruppel-associated box) subfamily of zinc finger proteins, which contain repeated Cys2-His2 (C2H2) zinc finger domains that are connected by conserved sequences, called H/C links. Transcriptional regulatory proteins containing tandemly repeated zinc finger domains are thought to be involved in both normal and abnormal cellular proliferation and differentiation. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 ZKSCAN1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Usf2IggmusPk HeLa USF2 IgM USF2 HeLa-S3 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001819 1819 GSM935561 Snyder Stanford PeakSeq1.0: We submit this dataset because of its high signal quality, although it narrowly missed the cut-off for replicate peak concordance hg19 exp wgEncodeSydhTfbsHelas3Usf2IggmusPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 USF2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tr4StdPk HeLa TR4 Std TR4 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000687 687 GSM935369 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Tr4StdPk None Peaks (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TR4 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tf3c110StdPk HeLa TF3C Std TFIIIC-110 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000747 747 GSM935342 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Tf3c110StdPk None Peaks TFIIIC-110 is a subunit of the RNA Polymerase III transcription factor TFIIIC. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 TFIIIC-110 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tcf7l2c9b92565UcdPk HeLa TCF7L2 UCD TCF7L2_C9B9_(2565) HeLa-S3 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-12-19 2012-09-18 wgEncodeEH002813 2813 GSM935625 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Tcf7l2c9b92565UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TCF7L2 C9B9 2565 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Tcf7l2UcdPk HeLa TCF7L2 UCD TCF7L2 HeLa-S3 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-19 2012-06-19 wgEncodeEH002069 2069 GSM816436 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Tcf7l2UcdPk None Peaks TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4 cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 TCF7L2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3TbpIggrabPk HeLa TBP IgR TBP HeLa-S3 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001790 1790 GSM935606 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3TbpIggrabPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 TBP IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Stat3IggrabPk HeLa STA3 IgR STAT3 HeLa-S3 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001799 1799 GSM935276 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Stat3IggrabPk None Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 STAT3 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Stat1Ifng30StdPk HeLa IFg3 STA1 Sd STAT1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000614 614 GSM935360 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3Stat1Ifng30StdPk IFNg30 Peaks transcription factor, activated by interferon signalling cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment HeLa-S3 STAT1 Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Spt20StdPk HeLa SPT Std SPT20 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001855 1855 GSM935615 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Spt20StdPk None Peaks Also known as FAM48A or P38IP. It is a component of SAGA complex. Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down-regulation of E-cadherin during gastrulation by regulating E-cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by Fgf signaling and Snail. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 SPT20 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Smc3ab9263IggrabPk HeLa SMC3 IgR SMC3_(ab9263) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001839 1839 GSM935384 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Smc3ab9263IggrabPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 SMC3 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Rpc155StdPk HeLa RPC1 Std RPC155 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000766 766 GSM935489 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Rpc155StdPk None Peaks polymerase (RNA) III (DNA directed) polypeptide A, 155kDa cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 RPC155 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Rfx5200401194IggrabPk HeLa RFX5 IgR RFX5_(200-401-194) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001818 1818 GSM935560 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Rfx5200401194IggrabPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 RFX5 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Rad21IggrabPk HeLa Rad2 IgR Rad21 HeLa-S3 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001789 1789 GSM935571 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Rad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Prdm19115IggrabPk HeLa PRDM IgR PRDM1_(9115) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001817 1817 GSM935555 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Prdm19115IggrabPk None Peaks Transcriptional repressor that binds specifically to the PRDI element in the promoter of the beta-interferon gene. Drives the maturation of B-lymphocytes into Ig secreting cells. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 PRDM1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Pol2s2IggrabPk HeLa PolS IgR Pol2(phosphoS2) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001838 1838 GSM935383 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Pol2s2IggrabPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 Pol2 S2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Pol2StdPk HeLa Pol2 Std Pol2 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000613 613 GSM935395 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3Pol2StdPk None Peaks RNA Polymerase II cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3P300sc584sc584IggrabPk HeLa p300 IgR p300_(SC-584) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001820 1820 GSM935500 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3P300sc584sc584IggrabPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 p300 SC584 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Nrf1IggmusPk HeLa Nrf1 IgM Nrf1 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000723 723 GSM935636 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Nrf1IggmusPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 Nrf1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3NfybIggrabPk HeLa NYB IgR NF-YB HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002067 2067 GSM935408 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3NfybIggrabPk None Peaks NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 NF-YB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3NfyaIggrabPk HeLa NYA IgR NF-YA HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002066 2066 GSM935508 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3NfyaIggrabPk None Peaks NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 NF-YA IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Mxi1af4185IggrabPk HeLa Mxi1 IgR Mxi1_(AF4185) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001826 1826 GSM935498 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Mxi1af4185IggrabPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 Mxi1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Mazab85725IggrabPk HeLa MAZ IgR MAZ_(ab85725) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002855 2855 GSM935272 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Mazab85725IggrabPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 MAZ IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3MaxStdPk HeLa Max Std Max HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000646 646 GSM935318 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3MaxStdPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 Max Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3MaxIggrabPk HeLa Max IgR Max HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002830 2830 GSM935405 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3MaxIggrabPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 Max IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3MafkIggrabPk HeLa MafK IgR MafK_(ab50322) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002856 2856 GSM935290 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3MafkIggrabPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 MafK IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3JundIggrabPk HeLa JunD IgR JunD HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000745 745 GSM935328 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3JundIggrabPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 JunD IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Irf3IggrabPk HeLa IRF3 IgR IRF3 HeLa-S3 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001788 1788 GSM935570 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Irf3IggrabPk None Peaks Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 IRF3 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Ini1IggmusPk HeLa INI1 IgM Ini1 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000722 722 GSM935635 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Ini1IggmusPk None Peaks Ini1 (BAF47, SMARCB1) is a ubiquitous 47 kD component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 INI1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Hcfc1nb10068209IggrabPk HeLa-S3 HCFC1 IgR HCFC1_(NB100-68209) HeLa-S3 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003389 3389 GSM1003618 Snyder Stanford exp wgEncodeSydhTfbsHelas3Hcfc1nb10068209IggrabPk None Peaks The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 HCFC1 (NB100-68209) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Hae2f1StdPk HeLa HAE2 Std HA-E2F1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000688 688 GSM935366 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Hae2f1StdPk None Peaks The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 HA-E2F1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Gtf2f1ab28179IggrabPk HeLa GT2F IgR GTF2F1_(AB28179) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001816 1816 GSM935554 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Gtf2f1ab28179IggrabPk None Peaks RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 GTF2F1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Gcn5StdPk HeLa GCN5 Std GCN5 HeLa-S3 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001849 1849 GSM935302 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Gcn5StdPk None Peaks KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4 cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 GCN5 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Elk4UcdPk HeLa ELK4 UCD ELK4 HeLa-S3 UCDavis ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001753 1753 GSM935351 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Elk4UcdPk None Peaks This gene is a member of the Ets family of transcription factors and of the ternary complex factor (TCF) subfamily. (provided by RefSeq) cervical carcinoma Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 ELK4 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Elk112771IggrabPk HeLa ELK1 IgR ELK1_(1277-1) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-12-01 wgEncodeEH002864 2864 GSM935326 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Elk112771IggrabPk None Peaks Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 ELK1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3E2f6StdPk HeLa E2F6 Std E2F6 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000692 692 GSM935476 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3E2f6StdPk None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 E2F6 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3E2f4StdPk HeLa E2F4 Std E2F4 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000689 689 GSM935365 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3E2f4StdPk None Peaks mapping at the C-terminus of E2F4 of human origin cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 E2F4 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3E2f1StdPk HeLa E2F1 Std E2F1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000699 699 GSM935484 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3E2f1StdPk None Peaks E2F1, the original member of the E2F family of transcription factors, was identified as a cellular protein with DNA binding activity associated with the adenovirus E2 gene promoter. E2F1 is cell cycle regulated with very low levels in early G1, then increasing levels as cells move from G1 to S, and highest levels of protein at the G1/S boundary, which is consistent with its role in S-phase entry. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 E2F1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Corestsc30189IggrabPk HeLa COREST IgR COREST_(sc-30189) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002844 2844 GSM935578 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsHelas3Corestsc30189IggrabPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 COREST SC30189 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CmycStdPk HeLa cMyc Std c-Myc HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000648 648 GSM935320 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3CmycStdPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 c-Myc Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CjunIggrabPk HeLa cJun IgR c-Jun HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000746 746 GSM935341 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3CjunIggrabPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 c-Jun IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Chd2IggrabPk HeLa CHD2 IgR CHD2_(AB68301) HeLa-S3 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002027 2027 GSM935432 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Chd2IggrabPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 CHD2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CfosStdPk HeLa cFOS Std c-Fos HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000647 647 GSM935317 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3CfosStdPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 c-FOS Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3CebpbIggrabPk HeLa CBPB IgR CEBPB HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001815 1815 GSM935553 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3CebpbIggrabPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 CEBPB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brg1IggmusPk HeLa BRG1 IgM Brg1 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000781 781 GSM935511 Snyder Yale hg18 exp wgEncodeSydhTfbsHelas3Brg1IggmusPk None Peaks Brg1 (SMARCA4) is an ATPase subunit of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment HeLa-S3 BRG1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brf2StdPk HeLa BRF2 Std BRF2 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000765 765 GSM935435 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Brf2StdPk None Peaks Brf2 is a component of an alternate form of the RNA Polymerase III transcription factor TFIIIB. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 BRF2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brf1StdPk HeLa BRF1 Std BRF1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000764 764 GSM935582 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Brf1StdPk None Peaks 'B-related factor 1', subunit of RNA polymerase III transcription initiation factor IIIB cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 BRF1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Brca1a300IggrabPk HeLa BRC1 IgR BRCA1_(A300-000A) HeLa-S3 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001814 1814 GSM935552 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsHelas3Brca1a300IggrabPk None Peaks Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. cervical carcinoma Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 BRCA1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Bdp1StdPk HeLa BDP1 Std BDP1 HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000763 763 GSM935486 Snyder Harvard hg18 exp wgEncodeSydhTfbsHelas3Bdp1StdPk None Peaks 'B double-prime 1', subunit of RNA polymerase III transcription initiation factor IIIB cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment HeLa-S3 BDP1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Baf170IggmusPk HeLa BAF7 IgM BAF170 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000721 721 GSM935638 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Baf170IggmusPk None Peaks BAF170 (SMARCC2, Brg1-Associated Factor, 170 kD) is a ubiquitous component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 BAF170 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Baf155IggmusPk HeLa BAF5 IgM BAF155 HeLa-S3 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000720 720 GSM935637 Snyder Stanford hg18 exp wgEncodeSydhTfbsHelas3Baf155IggmusPk None Peaks BAF155 (SMARCC1, Brg1-Associated Factor, 155 kD) is a ubiquitous component of the SWI/SNF chromatin-remodeling complex. cervical carcinoma Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment HeLa-S3 BAF155 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Ap2gammaStdPk HeLa AP2g Std AP-2gamma HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000686 686 GSM935370 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Ap2gammaStdPk None Peaks Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes. AP-2 factors bind to the consensus sequence 5'-GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development. They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 AP-2g Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsHelas3Ap2alphaStdPk HeLa AP2a Std AP-2alpha HeLa-S3 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000685 685 GSM935367 Snyder USC hg18 exp wgEncodeSydhTfbsHelas3Ap2alphaStdPk None Peaks Sequence-specific DNA-binding protein that interacts with inducible viral and cellular enhancer elements to regulate transcription of selected genes. AP-2 factors bind to the consensus sequence 5' -GCCNNNGGC-3' and activate genes involved in a large spectrum of important biological functions including proper eye, face, body wall, limb and neural tube development. They also suppress a number of genes including MCAM/MUC18, C/EBP alpha and MYC. AP-2alpha is the only AP-2 protein required for early morphogenesis of the lens vesicle (by similarity). cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment HeLa-S3 AP-2a Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549Rad21IggrabPk A549 Rad2 IgR Rad21 A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002822 2822 GSM935300 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549Rad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549Pol2s2IggrabPk A549 PolS IgR Pol2(phosphoS2) A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002821 2821 GSM935299 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549Pol2s2IggrabPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 Pol2 S2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549MaxIggrabPk A549 Max IgR Max A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002820 2820 GSM935298 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549MaxIggrabPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 Max IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549CtcfbIggrabPk A549 CTCF IgR CTCF_(SC-15914) A549 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003384 3384 GSM1003606 Snyder Stanford exp wgEncodeSydhTfbsA549CtcfbIggrabPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 CTCF (SC-15914) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549CmycIggrabPk A549 c-Myc IgR c-Myc A549 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003385 3385 GSM1003607 Snyder Stanford exp wgEncodeSydhTfbsA549CmycIggrabPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 c-Myc IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549CebpbIggrabPk A549 CBPB IgR CEBPB A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002818 2818 GSM935630 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549CebpbIggrabPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 CEBPB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsA549Bhlhe40IggrabPk A549 BHL4 IgR BHLHE40 A549 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002817 2817 GSM935440 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsA549Bhlhe40IggrabPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment A549 BHLHE40 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znfmizdcp1ab65767IggrabPk K562 ZNF-MIZD IgR ZNF-MIZD-CP1_(ab65767) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003381 3381 GSM1003611 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Znfmizdcp1ab65767IggrabPk None Peaks Zinc finger MIZ domain-containing protein 1 that increases ligand-dependent transcriptional activity of AR and promotes AR sumoylation. The stimulation of AR activity is dependent upon sumoylation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 ZNF-MIZD-CP1 (ab65767) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf384hpa004051IggrabPk K562 ZNF384 IgR ZNF384_(HPA004051) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003382 3382 GSM1003621 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Znf384hpa004051IggrabPk None Peaks This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 ZNF384 (HPA004051) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf274m01UcdPk K562 Z274M UCD ZNF274_(M01) K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-09-14 2012-06-14 wgEncodeEH002068 2068 GSM935503 Snyder USC PeakSeq1.0. This factor has a limited number of highly enriched target sites and for factors with so few binding sites, we believe that in order to get a good overlap between replicate datasets one must have fewer reads.  We are confident with the overlap of the highly enriched binding sites for this dataset regardless of the poor replicate overlap. hg19 exp wgEncodeSydhTfbsK562Znf274m01UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor and interacts with the KAP1 corepressor complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 ZNF274 (M01) UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf274UcdPk K562 Z274 UCD ZNF274 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000696 696 GSM935479 Snyder USC hg18 exp wgEncodeSydhTfbsK562Znf274UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 ZNF274 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf263UcdPk K562 Z263 UCD ZNF263 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000630 630 GSM935532 Snyder USC hg18 exp wgEncodeSydhTfbsK562Znf263UcdPk None Peaks ZNF263 (NP_005732, 201 a.a. ~ 299 a.a) partial recombinant protein with GST tag. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 ZNF263 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Znf143IggrabPk K562 Z143 IgR Znf143_(16618-1-AP) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002030 2030 GSM935568 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Znf143IggrabPk None Peaks Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Znf143 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Zc3h11anb10074650IggrabPk K562 ZC3H11A IgR ZC3H11A_(NB100-74650) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEH003380 3380 GSM1003610 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Zc3h11anb10074650IggrabPk None Peaks ZC3H11A is a C3H1-type zinc finger protein. ZC3H11A has been identified as a protein that is phosphorylated upon DNA damage by ATM or ATR. The function of ZC3H11A remains uncharacterized. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 ZC3H11A (NB100-74650) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Yy1UcdPk K562 YY1 UCD YY1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000684 684 GSM935368 Snyder USC hg18 exp wgEncodeSydhTfbsK562Yy1UcdPk None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 YY1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Xrcc4StdPk K562 XRCC Std XRCC4 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000650 650 GSM935425 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Xrcc4StdPk None Peaks Recognizes the XRCC4 protein (X ray cross complementation protein). XRCC4 is a ubiquitous protein reported to have a role in DNA double-stranded break repair and in V(D)J recombination. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 XRCC4 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Usf2IggrabPk K562 USF2 IgR USF2 K562 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001797 1797 GSM935356 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Usf2IggrabPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 USF2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ubtfsab1404509IggmusPk K562 UBTF IgM UBTF_(SAB1404509) K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002850 2850 GSM935642 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Ubtfsab1404509IggmusPk None Peaks Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 UBTF IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ubfsc13125IggmusPk K562 UBF IgM UBF_(sc-13125) K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002863 2863 GSM935338 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Ubfsc13125IggmusPk None Peaks Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 UBF IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tr4UcdPk K562 TR4 UCD TR4 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000682 682 GSM935374 Snyder USC hg18 exp wgEncodeSydhTfbsK562Tr4UcdPk None Peaks (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 TR4 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tf3c110StdPk K562 TF3C Std TFIIIC-110 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000748 748 GSM935343 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Tf3c110StdPk None Peaks TFIIIC-110 is a subunit of the RNA Polymerase III transcription factor TFIIIC. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 TFIIIC-110 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562TbpIggmusPk K562 TBP IgM TBP K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001825 1825 GSM935495 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562TbpIggmusPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 TBP IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tblr1nb600270IggrabPk K562 TBLR1 IgR TBLR1_(NB600-270) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002848 2848 GSM935574 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Tblr1nb600270IggrabPk None Peaks F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 TBLR1 NB600270 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tblr1ab24550IggrabPk K562 TBLR1 IgR TBLR1_(ab24550) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002849 2849 GSM935575 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Tblr1ab24550IggrabPk None Peaks F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 TBLR1 AB24550 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Tal1sc12984IggmusPk K562 TAL1 IgM TAL1_(SC-12984) K562 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001824 1824 GSM935496 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Tal1sc12984IggmusPk None Peaks TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 TAL1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat2Ifna6hStdPk K562 IFa6 STA2 Sd STAT2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000666 666 GSM935469 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat2Ifna6hStdPk IFNa6h Peaks peptide mapping at c-terminus of Human STAT2 p-113 (C-20) X leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 STAT2 Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat2Ifna30StdPk K562 IFa3 STA2 Sd STAT2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000665 665 GSM935470 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat2Ifna30StdPk IFNa30 Peaks peptide mapping at c-terminus of Human STAT2 p-113 (C-20) X leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 STAT2 Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifng6hStdPk K562 IFg6 STA1 Sd STAT1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000761 761 GSM935488 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Stat1Ifng6hStdPk IFNg6h Peaks transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 STAT1 Standard IFNg 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifng30StdPk K562 IFg3 STA1 Sd STAT1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000760 760 GSM935487 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Stat1Ifng30StdPk IFNg30 Peaks transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 STAT1 Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifna6hStdPk K562 IFa6 STA1 Sd STAT1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000664 664 GSM935471 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat1Ifna6hStdPk IFNa6h Peaks transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 STAT1 Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Stat1Ifna30StdPk K562 IFa3 STA1 Sd STAT1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000663 663 GSM935472 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Stat1Ifna30StdPk IFNa30 Peaks transcription factor, activated by interferon signalling leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 STAT1 Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Smc3ab9263IggrabPk K562 SMC3 IgR SMC3_(ab9263) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001845 1845 GSM935310 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Smc3ab9263IggrabPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 SMC3 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Sirt6StdPk K562 SIRT Std SIRT6 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000681 681 GSM935371 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Sirt6StdPk None Peaks A synthetic peptide made to an internal region of the human SIRT6 protein leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 SIRT6 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Setdb1UcdPk K562 STDB UCD SETDB1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000677 677 GSM935598 Snyder USC hg18 exp wgEncodeSydhTfbsK562Setdb1UcdPk None Peaks SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 SETDB1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Setdb1MnasedUcdPk K562 MNas STDB UC SETDB1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000769 769 GSM935573 Snyder USC hg18 exp wgEncodeSydhTfbsK562Setdb1MnasedUcdPk MNaseD Peaks SET domain, bifurcated 1, the SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Fragmented using micrococcal nuclease digestion Regions of enriched signal in experiment K562 SETDB1 UC Davis MNaseD ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Rpc155StdPk K562 RPC1 Std RPC155 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000680 680 GSM935372 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Rpc155StdPk None Peaks polymerase (RNA) III (DNA directed) polypeptide A, 155kDa leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 RPC155 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Rfx5IggrabPk K562 RFX5 IgR RFX5_(200-401-194) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-30 wgEncodeEH002033 2033 GSM935565 Snyder Stanford PeakSeq1.0.  Although this dataset narrowly misses the ENCODE cut-off for peak agreement between replicates, the exceptionally strong signals observed at the HLA loci on chromosome 6 indicate that this is a high-quality dataset. hg19 exp wgEncodeSydhTfbsK562Rfx5IggrabPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 RFX5 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Rad21StdPk K562 Rad2 Std Rad21 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000649 649 GSM935319 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Rad21StdPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 Rad21 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol3StdPk K562 Pol3 Std Pol3 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000694 694 GSM935481 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Pol3StdPk None Peaks RNA Polymerase III leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 POL3 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2s2StdPk K562 PolS Std Pol2(phosphoS2) K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-07-12 2011-04-12 wgEncodeEH001805 1805 GSM935645 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Pol2s2StdPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Pol2 S2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2s2IggrabPk K562 PolS IgR Pol2(phosphoS2) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002833 2833 GSM935402 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Pol2s2IggrabPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Pol2 S2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2StdPk K562 Pol2 Std Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000616 616 GSM935358 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2StdPk None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifng6hStdPk K562 IFg6 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000662 662 GSM935473 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2Ifng6hStdPk IFNg6h Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 Pol2 Standard IFNg 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifng30StdPk K562 IFg3 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000704 704 GSM935388 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Pol2Ifng30StdPk IFNg30 Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 Pol2 Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifna6hStdPk K562 IFa6 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000661 661 GSM935474 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2Ifna6hStdPk IFNa6h Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 Pol2 Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2Ifna30StdPk K562 IFa3 Pol2 Sd Pol2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000660 660 GSM935475 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Pol2Ifna30StdPk IFNa30 Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 Pol2 Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Pol2IggmusPk K562 Pol2 IgM Pol2 K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000727 727 GSM935632 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Pol2IggmusPk None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562P300sc584sc48343IggrabPk K562 p300 IgR p300_(SC-48343) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001828 1828 GSM935494 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562P300sc584sc48343IggrabPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 p300 SC48343 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562P300IggrabPk K562 p300 IgR p300 K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002834 2834 GSM935401 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562P300IggrabPk None Peaks EP300(c-20) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 p300 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Nrf1IggrabPk K562 Nrf1 IgR Nrf1 K562 IgG-rab ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001796 1796 GSM935361 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Nrf1IggrabPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Nrf1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562NfybStdPk K562 NYB Std NF-YB K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002024 2024 GSM935429 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562NfybStdPk None Peaks NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 NF-YB Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562NfyaStdPk K562 NYA Std NF-YA K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-22 2012-03-22 wgEncodeEH002021 2021 GSM935433 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562NfyaStdPk None Peaks NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 NF-YA Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Nfe2StdPk K562 NFE2 Std NF-E2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000624 624 GSM935414 Snyder Yale hg18 exp wgEncodeSydhTfbsK562Nfe2StdPk None Peaks Nuclear factor, erythroid-derived 2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 NF-E2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562NelfeStdPk K562 NELF Std NELFe K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000701 701 GSM935392 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562NelfeStdPk None Peaks NELF-E (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 NELFe Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Mxi1af4185IggrabPk K562 Mxi1 IgR Mxi1_(AF4185) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-27 2011-07-27 wgEncodeEH001827 1827 GSM935497 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Mxi1af4185IggrabPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Mxi1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Mazab85725IggrabPk K562 MAZ IgR MAZ_(ab85725) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002862 2862 GSM935337 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Mazab85725IggrabPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 MAZ IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562MaxStdPk K562 Max Std Max K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000637 637 GSM935539 Snyder Yale hg18 exp wgEncodeSydhTfbsK562MaxStdPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 Max Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562MaxIggrabPk K562 Max IgR Max K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEH002869 2869 GSM935344 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562MaxIggrabPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Max IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Mafkab50322IggrabPk K562 MafK IgR MafK_(ab50322) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001844 1844 GSM935311 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Mafkab50322IggrabPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 MafK IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562MaffIggrabPk K562 MafF IgR MafF_(M8194) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002804 2804 GSM935520 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562MaffIggrabPk None Peaks The protein encoded by this gene is a (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. Can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. May also be involved in the cellular stress response. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 MafF IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Kap1UcdPk K562 KAP1 UCD KAP1 K562 UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-08-23 2011-05-23 wgEncodeEH001764 1764 GSM935464 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Kap1UcdPk None Peaks KRAB Associated Protein 1, helps regulate transcriptional repression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 KAP1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562JundIggrabPk K562 JunD IgR JunD K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002164 2164 GSM935569 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562JundIggrabPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 JunD IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifng6hStdPk K562 IFg6 IRF1 Sd IRF1 K562 std ChipSeq ENCODE June 2010 Freeze 2010-04-29 2011-01-29 wgEncodeEH001866 1866 GSM935549 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Irf1Ifng6hStdPk IFNg6h Peaks Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 IRF1 Standard IFNg 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifng30StdPk K562 IFg3 IRF1 Sd IRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002799 2799 GSM935505 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Irf1Ifng30StdPk IFNg30 Peaks Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 IRF1 Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifna6hStdPk K562 IFa6 IRF1 Sd IRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002798 2798 GSM935504 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Irf1Ifna6hStdPk IFNa6h Peaks Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 IRF1 Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Irf1Ifna30StdPk K562 IFa3 IRF1 Sd IRF1 K562 std ChipSeq ENCODE June 2010 Freeze 2010-04-29 2011-01-29 wgEncodeEH001865 1865 GSM935546 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Irf1Ifna30StdPk IFNa30 Peaks Interferon regulatory factor 1 is a member of the interferon regulatory transcription factor (IRF) family. IRF1 serves as an activator of interferons alpha and beta transcription and also functions as a transcription activator of genes induced by interferons alpha, beta, and gamma. IRF1 has been shown to play roles in regulating apoptosis and tumor suppression. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 IRF1 Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ini1IggmusPk K562 INI1 IgM Ini1 K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000725 725 GSM935634 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Ini1IggmusPk None Peaks Ini1 (BAF47, SMARCB1) is a ubiquitous 47 kD component of the SWI/SNF chromatin-remodeling complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 INI1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Hmgn3StdPk K562 HMGN Std HMGN3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001863 1863 GSM935544 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Hmgn3StdPk None Peaks HMGN3 is a high-mobility group protein. These proteins are small, 8 to 11 kDa, ubiquitous proteins believed to play a role in chromatin structure. HMGNs bind to nucleosomes between the histone core and DNA and reduce chromatin compaction. As a result HMGNs, HMGN3 included, are believed to increase access to DNA for DNA replication, repair and transcription. HMGN3 has specifically been implicated in the action of Thyroid horomone receptors. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 HMGN3 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Hcfc1nb10068209IggrabPk K562 HCFC1 IgR HCFC1_(NB100-68209) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003392 3392 GSM1003625 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Hcfc1nb10068209IggrabPk None Peaks The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 HCFC1 (NB100-68209) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gtf2f1ab28179IggrabPk K562 GT2F IgR GTF2F1_(AB28179) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001823 1823 GSM935501 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Gtf2f1ab28179IggrabPk None Peaks RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 GTF2F1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gtf2bStdPk K562 GT2B Std GTF2B K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-01-11 2010-10-11 wgEncodeEH000703 703 GSM935394 Snyder Harvard PeakSeq1.0 hg18 exp wgEncodeSydhTfbsK562Gtf2bStdPk None Peaks DNA- binding general transcription factor leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 GTF2B Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gata2UcdPk K562 GAT2 UCD GATA-2 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000683 683 GSM935373 Snyder USC hg18 exp wgEncodeSydhTfbsK562Gata2UcdPk None Peaks GATA binding protein 2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 GATA2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gata1bIggmusPk K562 GATA1 IgM GATA1_(SC-266) K562 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003368 3368 GSM1003608 Snyder Stanford exp wgEncodeSydhTfbsK562Gata1bIggmusPk None Peaks GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 GATA1 (SC-266) IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Gata1UcdPk K562 GAT1 UCD GATA-1 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000638 638 GSM935540 Snyder USC hg18 exp wgEncodeSydhTfbsK562Gata1UcdPk None Peaks GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 GATA1 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Elk112771IggrabPk K562 ELK1 IgR ELK1_(1277-1) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-03-01 2012-12-01 wgEncodeEH003356 3356 GSM1003620 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Elk112771IggrabPk None Peaks Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 ELK1 (1277-1) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562E2f6UcdPk K562 E2F6 UCD E2F6 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000676 676 GSM935597 Snyder USC hg18 exp wgEncodeSydhTfbsK562E2f6UcdPk None Peaks This gene encodes a member of the E2F transcription factor protein family. E2F family members play a crucial role in control of the cell cycle and of the action of tumor suppressor proteins. They are also a target of the transforming proteins of small DNA tumor viruses. Many E2F proteins contain several evolutionarily conserved domains: a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. The encoded protein of this gene is atypical because it lacks the transactivation and tumor suppressor protein association domains. It contains a modular suppression domain and is an inhibitor of E2F-dependent transcription. The protein is part of a multimeric protein complex that contains a histone methyltransferase and the transcription factors Mga and Max. Multiple transcript variants have been reported for this gene, but it has not been clearly demonstrated that they encode valid isoforms (RefSeq). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 E2F6 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562E2f4UcdPk K562 E2F4 UCD E2F4 K562 UCDavis ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000671 671 GSM935600 Snyder USC hg18 exp wgEncodeSydhTfbsK562E2f4UcdPk None Peaks mapping at the C-terminus of E2F4 of human origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment K562 E2F4 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CtcfbIggrabPk K562 CTCF IgR CTCF_(SC-15914) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002797 2797 GSM935407 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562CtcfbIggrabPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 CTCF IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Corestsc30189IggrabPk K562 COREST IgR COREST_(sc-30189) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-01-22 2012-10-21 wgEncodeEH002814 2814 GSM935439 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Corestsc30189IggrabPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 COREST SC30189 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Corestab24166IggrabPk K562 COREST IgR COREST_(ab24166) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002847 2847 GSM935385 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Corestab24166IggrabPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 COREST AB24166 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycStdPk K562 cMyc Std c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000621 621 GSM935410 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycStdPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 c-Myc Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfng6hStdPk K562 IFg6 cMyc Sd c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000670 670 GSM935599 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycIfng6hStdPk IFNg6h Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 c-Myc Standard IFNg 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfng30StdPk K562 IFg3 cMyc Sd c-Myc K562 std ChipSeq ENCODE Jan 2011 Freeze 2010-08-17 2011-05-17 wgEncodeEH001867 1867 GSM935548 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562CmycIfng30StdPk IFNg30 Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 c-Myc Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfna6hStdPk K562 IFa6 cMyc Sd c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000669 669 GSM935466 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycIfna6hStdPk IFNa6h Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 c-Myc Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIfna30StdPk K562 IFa3 cMyc Sd c-Myc K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000659 659 GSM935428 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CmycIfna30StdPk IFNa30 Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 c-Myc Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CmycIggrabPk K562 cMyc IgR c-Myc K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002800 2800 GSM935516 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562CmycIggrabPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 c-Myc IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunStdPk K562 cJun Std c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000620 620 GSM935411 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunStdPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 c-Jun Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfng6hStdPk K562 IFg6 cJun Sd c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000668 668 GSM935467 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunIfng6hStdPk IFNg6h Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 c-Jun Standard IFNg 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfng30StdPk K562 IFg3 cJun Sd c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000673 673 GSM935602 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunIfng30StdPk IFNg30 Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon gamma treatment - 30 minutes (Snyder) Regions of enriched signal in experiment K562 c-Jun Standard IFNg 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfna6hStdPk K562 IFa6 cJun Sd c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000667 667 GSM935468 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CjunIfna6hStdPk IFNa6h Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Interferon alpha treatment - 6 hours (Snyder) Regions of enriched signal in experiment K562 c-Jun Standard IFNa 6hrs ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIfna30StdPk K562 IFa3 cJun Sd c-Jun K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002805 2805 GSM935521 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562CjunIfna30StdPk IFNa30 Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University 30 m of Interferon alpha (Snyder) Regions of enriched signal in experiment K562 c-Jun Standard IFNa 30min ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CjunIggrabPk K562 c-Jun IgR c-Jun K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003369 3369 GSM1003609 Snyder Stanford exp wgEncodeSydhTfbsK562CjunIggrabPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 c-Jun IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Chd2ab68301IggrabPk K562 CHD2 IgR CHD2_(AB68301) K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001822 1822 GSM935502 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Chd2ab68301IggrabPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 CHD2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CfosStdPk K562 cFOS Std c-Fos K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-09 2012-03-09 wgEncodeEH000619 619 GSM935355 Snyder Yale hg18 exp wgEncodeSydhTfbsK562CfosStdPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment K562 c-FOS Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562CebpbIggrabPk K562 CBPB IgR CEBPB K562 IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001821 1821 GSM935499 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562CebpbIggrabPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 CEBPB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Cdpsc6327IggrabPk K562 CDP IgR CDP_(sc-6327) K562 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003391 3391 GSM1003622 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Cdpsc6327IggrabPk None Peaks CDP (for CCAAT displacement protein) was identified as a repressor for tran- scription of developmentally regulated genes. It is a homeodomain protein that appears to compete with transcriptional activating proteins for binding to the promoter regions of various genes. CDP contains three cut repeats which function as DNA binding domains. It has been demonstrated that cut repeat domains have the capacity to bind to DNA in conjunction with or independently of homeodomain DNA binding. CDP has been shown to be the DNA-binding subunit of the HiNF-D complex, which contains cyclin A, Cdc2 and an Rb-related protein in addition to CDP. Histone expression is required for the transition to S phase in the cell cycle. The HiNF-D complex regulates the transcription of Histone H4, H3 and H1 genes, allowing cells to progress from G1 to S phase. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 CDP (SC-6327) IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Ccnt2StdPk K562 CNT2 Std CCNT2 K562 std ChipSeq ENCODE June 2010 Freeze 2010-04-28 2011-01-28 wgEncodeEH001864 1864 GSM935547 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Ccnt2StdPk None Peaks CycT2 is one of three cyclins that can form a heterodimer with cyclin-dependent kinase 9 (CDK9). The heterodimer is known as positive elongation factor b (P-TEFb) and is responsible for the phosphophorylation of Ser2 of the heptad repeat in the C-terminal domain of RNA polymerase II as well as the negative elongation factors DSIF (hSpt4/hSpt5) and NELF. Phosphorylation of RNA polymerase II and the negative elongation factors by P-TEFb promotes elongation. CycT2 contains a leucine rich domain capable of binding to the C-terminal domain of RNA polymerase II. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 CCNT2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Brg1IggmusPk K562 BRG1 IgM Brg1 K562 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000724 724 GSM935633 Snyder Stanford hg18 exp wgEncodeSydhTfbsK562Brg1IggmusPk None Peaks Brg1 (SMARCA4) is an ATPase subunit of the SWI/SNF chromatin-remodeling complex. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 BRG1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Brf2StdPk K562 BRF2 Std BRF2 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000767 767 GSM935490 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Brf2StdPk None Peaks Brf2 is a component of an alternate form of the RNA Polymerase III transcription factor TFIIIB. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 BRF2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Brf1StdPk K562 BRF1 Std BRF1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000679 679 GSM935595 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Brf1StdPk None Peaks 'B-related factor 1', subunit of RNA polymerase III transcription initiation factor IIIB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 BRF1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Bhlhe40nb100IggrabPk K562 BHL4 IgR BHLHE40_(NB100-1800) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEH001857 1857 GSM935616 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsK562Bhlhe40nb100IggrabPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 BHLHE40 NB100 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Bdp1StdPk K562 BDP1 Std BDP1 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000678 678 GSM935594 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Bdp1StdPk None Peaks 'B double-prime 1', subunit of RNA polymerase III transcription initiation factor IIIB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 BDP1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Bach1sc14700IggrabPk K562 Bach1 IgR Bach1_(sc-14700) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002846 2846 GSM935576 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Bach1sc14700IggrabPk None Peaks This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 Bach1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Atf3StdPk K562 ATF3 Std ATF3 K562 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000700 700 GSM935391 Snyder Harvard hg18 exp wgEncodeSydhTfbsK562Atf3StdPk None Peaks Activating transcription factor 3. A bZIP transcription factor and member of the Ca2+/cAMP response element-binding (CREB) protein family. ATF3 is found to act both as an activator and repressor of transcription. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 ATF3 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Atf106325StdPk K562 ATF1 Std ATF1_(06-325) K562 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-13 2012-12-13 wgEncodeEH002865 2865 GSM935340 Snyder Harvard PeakSeq1.0 exp wgEncodeSydhTfbsK562Atf106325StdPk None Peaks ATF1 is a bZip transcription factor from the CREB family. ATF1 binds to both cAMP response elements (TGACGTCA). leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment K562 ATF1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsK562Arid3asc8821IggrabPk K562 ARI3 IgR ARID3A_(sc-8821) K562 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002861 2861 GSM935336 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsK562Arid3asc8821IggrabPk None Peaks This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. (provided by RefSeq) leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment K562 ARID3A SC8821 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescZnf274m01UcdPk H1ES ZNF274 UCD ZNF274_(M01) H1-hESC UCDavis ChipSeq ENCODE Jul 2012 Freeze 2012-06-06 2013-03-05 wgEncodeEH003357 3357 GSM1003619 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsH1hescZnf274m01UcdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor and interacts with the KAP1 corepressor complex. embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment H1-hESC ZNF274 (M01) UC Davis ChIP-seq Peaks from ENCODE/USC Regulation 
wgEncodeSydhTfbsH1hescZnf143IggrabPk H1ES Z143 IgR Znf143_(16618-1-AP) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002802 2802 GSM935514 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescZnf143IggrabPk None Peaks Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC Znf143 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescUsf2IggrabPk H1ES USF2 IgR USF2 H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001837 1837 GSM935380 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescUsf2IggrabPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC USF2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescTbpIggrabPk H1ES TBP IgR TBP H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001848 1848 GSM935303 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescTbpIggrabPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC TBP IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescSuz12UcdPk H1ES SZ12 UCD SUZ12 H1-hESC UCDavis ChipSeq ENCODE June 2010 Freeze 2010-04-27 2011-01-27 wgEncodeEH001752 1752 GSM935352 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescSuz12UcdPk None Peaks Suppressor of zeste 12 homolog, Polycomb group (PcG) protein, Component of the PRC2/EED-EZH2 complex embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment H1-hESC SUZ12 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescSin3anb6001263IggrabPk H1ES SIN3A IgR SIN3A_(NB600-1263) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002854 2854 GSM935289 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescSin3anb6001263IggrabPk None Peaks Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid &amp; thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR). embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC SIN3A IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescRfx5200401194IggrabPk H1ES RFX5 IgR RFX5_(200-401-194) H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001835 1835 GSM935382 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescRfx5200401194IggrabPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC RFX5 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescRad21IggrabPk H1ES Rad2 IgR Rad21 H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001836 1836 GSM935379 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescRad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescNrf1IggrabPk H1ES Nrf1 IgR Nrf1 H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-18 wgEncodeEH001847 1847 GSM935308 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescNrf1IggrabPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC Nrf1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescMxi1IggrabPk H1ES Mxi1 IgR Mxi1_(AF4185) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002829 2829 GSM935293 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescMxi1IggrabPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC Mxi1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescMaxUcdPk H1ES Max UCD Max H1-hESC UCDavis ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH001757 1757 GSM935348 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescMaxUcdPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment H1-hESC Max UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescMafkIggrabPk H1ES MafK IgR MafK_(ab50322) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002828 2828 GSM935292 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescMafkIggrabPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC MafK IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescJundIggrabPk H1ES JunD IgR JunD H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-27 2012-03-27 wgEncodeEH002023 2023 GSM935434 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescJundIggrabPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC JunD IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescGtf2f1IggrabPk H1ES GT2F IgR GTF2F1_(AB28179) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002843 2843 GSM935581 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescGtf2f1IggrabPk None Peaks RNA polymerase II transcription factor TFIIF is a heterodimer with 2 subunits: one, referred to as RAP74. TFIIF appears to assist TFIIB in recruiting RNA polymerase II into a preinitiation complex. It also affects RNA transcription by suppressing transient pausing of the polymerase at locations on the DNA template. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC GTF2F1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCtbp2UcdPk H1ES CBP2 UCD CtBP2 H1-hESC UCDavis ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001767 1767 GSM935463 Snyder USC PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescCtbp2UcdPk None Peaks C-terminal binding protein 2 embryonic stem cells Input library was prepared at UC Davis. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment H1-hESC CtBP2 UC Davis ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCmycIggrabPk H1ES cMyc IgR c-Myc H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-28 2012-06-28 wgEncodeEH002795 2795 GSM935509 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescCmycIggrabPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC c-Myc IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCjunIggrabPk H1ES cJun IgR c-Jun H1-hESC IgG-rab ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-19 wgEncodeEH001854 1854 GSM935614 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsH1hescCjunIggrabPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC c-Jun IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescChd2IggrabPk H1ES CHD2 IgR CHD2_(AB68301) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002827 2827 GSM935297 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescChd2IggrabPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC CHD2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescChd1a301218aIggrabPk H1ES CHD1 IgR CHD1_(A301-218A) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002826 2826 GSM935296 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescChd1a301218aIggrabPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC CHD1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescCebpbIggrabPk H1ES CBPB IgR CEBPB H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002825 2825 GSM935295 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescCebpbIggrabPk None Peaks Epitope mapping at the C-terminus of C/EBP-beta of rat origin embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC CEBPB IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescBrca1IggrabPk H1ES BRC1 IgR BRCA1_(A300-000A) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEH002801 2801 GSM935517 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescBrca1IggrabPk None Peaks Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC BRCA1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsH1hescBach1sc14700IggrabPk H1ES Bach1 IgR Bach1_(sc-14700) H1-hESC IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002842 2842 GSM935580 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsH1hescBach1sc14700IggrabPk None Peaks This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. (provided by RefSeq) embryonic stem cells Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment H1-hESC Bach1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Zzz3StdPk GM78 ZZZ3 Std ZZZ3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000698 698 GSM935483 Snyder Harvard hg18 exp wgEncodeSydhTfbsGm12878Zzz3StdPk None Peaks ZZZ3 contains one ZZ-type zinc finger domain. ZZ type finger domains are named because of their ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions -they are most likely involved in ligand binding or molecular scaffolding. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment GM12878 ZZZ3 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Znf384hpa004051IggmusPk GM78 ZNF384 IgM ZNF384_(HPA004051) GM12878 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003388 3388 GSM1003602 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Znf384hpa004051IggmusPk None Peaks This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 ZNF384 (HPA004051) IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Znf274StdPk GM78 Z274 Std ZNF274 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-05-20 2011-02-20 wgEncodeEH001756 1756 GSM935349 Snyder USC PeakSeq1.0.  Replicate overlap below cutoff, but submitted because there are very few biologically real targets and all the targets are in heterochromatic regions. hg19 exp wgEncodeSydhTfbsGm12878Znf274StdPk None Peaks ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor. It localizes predominantly to the nucleolus. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment GM12878 ZNF274 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Znf143166181apStdPk GM78 Z143 Std Znf143_(16618-1-AP) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001853 1853 GSM935613 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Znf143166181apStdPk None Peaks Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates to efficient U6 RNA polymerase III transcription via its interaction with CHD8 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Znf143 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Yy1StdPk GM78 YY1 Std YY1 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000695 695 GSM935482 Snyder USC hg18 exp wgEncodeSydhTfbsGm12878Yy1StdPk None Peaks YIN YANG 1 transcription factor belongs to the GLI-Kruppel class of zinc finger proteins. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment GM12878 YY1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878WhipIggmusPk GM78 WHIP IgM WHIP GM12878 IgG-mus ChipSeq ENCODE June 2010 Freeze 2010-04-26 2011-01-26 wgEncodeEH001787 1787 GSM935492 Snyder Stanford PeakSeq1.0. Although this dataset barely misses the establish ENCODE standard for data agreement with 77% agreement between replicates instead of 80%, we have submitted it because it appears to be of high quality and because it is from the GM12878 cell line where we and others have generally observed weaker ChIP signal. hg19 exp wgEncodeSydhTfbsGm12878WhipIggmusPk None Peaks Interacts with the N-terminal portion of Werner protein containing the exonuclease domain, shows homology to replication factor C family proteins, and is conserved from E. coli to human. Studies in yeast suggest that this gene may influence the aging process. Functions as a modulator for initiation or reinitiation events during DNA polymerase delta-mediated DNA synthesis. Has an intrinsic ATPase activity that functions as a sensor of DNA damage or of arrested replication forks and regulates the extent of DNA synthesis. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 WHIP IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Usf2IggmusPk GM78 USF2 IgM USF2 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001812 1812 GSM935558 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Usf2IggmusPk None Peaks Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3'). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 USF2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Tr4StdPk GM78 TR4 Std TR4 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000697 697 GSM935480 Snyder USC hg18 exp wgEncodeSydhTfbsGm12878Tr4StdPk None Peaks (Also: NR2C2) Members of the nuclear hormone receptor family, such as NR2C2, act as ligand-activated transcription factors. The proteins have an N-terminal transactivation domain, a central DNA-binding domain with 2 zinc fingers, and a ligand-binding domain at the C terminus. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment GM12878 TR4 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878TbpIggmusPk GM78 TBP IgM TBP GM12878 IgG-mus ChipSeq ENCODE June 2010 Freeze 2010-06-11 2011-03-11 wgEncodeEH001798 1798 GSM935277 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878TbpIggmusPk None Peaks General transcription factor that functions at the core of the DNA-binding multiprotein factor TFIID. Binding of TFIID to the TATA box is the initial transcriptional step of the pre-initiation complex (PIC), playing a role in the activation of eukaryotic genes transcribed by RNA polymerase II. Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 TBP IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusPk GM78 TBLR1 IgM TBLR1_(ab24550) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002853 2853 GSM935653 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusPk None Peaks F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 TBLR1 AB24550 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Stat3IggmusPk GM78 STA3 IgM STAT3 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001811 1811 GSM935557 Snyder Stanford PeakSeq1.0.  Because of the common difficulty in achieving good signal strength with the GM12878 cell line, we submit this dataset although it narrowly missed the peak concordance standard. hg19 exp wgEncodeSydhTfbsGm12878Stat3IggmusPk None Peaks Member of STAT family. After phosphorylation in response to cytokines and growth factors (including IFNs, EGF, IL5, IL6, HGF, LIF and BMP2), forms homo- or heterodimers that translocate to nucleus and activate transcription. Activates expression of a variety of genes with roles in processes such as cell growth and apoptosis. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 STAT3 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Stat1StdPk GM78 STA1 Std STAT1 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-20 wgEncodeEH001852 1852 GSM935612 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Stat1StdPk None Peaks transcription factor, activated by interferon signalling B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 STAT1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Srebp2IggrabPk GM78 SREBP2 IgR SREBP2 GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003363 3363 GSM1003603 Snyder Stanford exp wgEncodeSydhTfbsGm12878Srebp2IggrabPk None Peaks Sterol regulatory element binding transcription factor 2 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 SREBP2 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Srebp1IggrabPk GM78 SREBP1 IgR SREBP1 GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003362 3362 GSM1003617 Snyder Stanford exp wgEncodeSydhTfbsGm12878Srebp1IggrabPk None Peaks Sterol regulatory element binding transcription factor 1 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 SREBP1 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Spt20StdPk GM78 SPT Std SPT20 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001873 1873 GSM935417 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Spt20StdPk None Peaks Also known as FAM48A or P38IP. It is a component of SAGA complex. Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down-regulation of E-cadherin during gastrulation by regulating E-cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by Fgf signaling and Snail. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment GM12878 SPT20 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Smc3ab9263IggmusPk GM78 SMC3 IgM SMC3_(ab9263) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001833 1833 GSM935376 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Smc3ab9263IggmusPk None Peaks Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 SMC3 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Sin3anb6001263IggmusPk GM78 SIN3A IgM SIN3A_(NB600-1263) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEH002868 2868 GSM935331 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Sin3anb6001263IggmusPk None Peaks Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid &amp; thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 SIN3A IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Rfx5200401194IggmusPk GM78 RFX5 IgM RFX5_(200-401-194) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001810 1810 GSM935556 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Rfx5200401194IggmusPk None Peaks Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 RFX5 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Rad21IggrabPk GM78 Rad2 IgR Rad21 GM12878 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000749 749 GSM935332 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12878Rad21IggrabPk None Peaks Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Rad21 IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol3StdPk GM78 Pol3 Std Pol3 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000645 645 GSM935316 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878Pol3StdPk None Peaks RNA Polymerase III B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment GM12878 POL3 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol2s2IggmusPk GM78 PolS IgM Pol2(phosphoS2) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-03-31 2011-12-31 wgEncodeEH001858 1858 GSM935608 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Pol2s2IggmusPk None Peaks RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Pol2 S2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol2StdPk GM78 Pol2 Std Pol2 GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000626 626 GSM935412 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878Pol2StdPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment GM12878 Pol2 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Pol2IggmusPk GM78 Pol2 IgM Pol2 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000708 708 GSM935386 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12878Pol2IggmusPk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Pol2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878P300bStdPk GM78 p300 Std p300_(SC-584) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002037 2037 GSM935562 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878P300bStdPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 p300 SC584 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878P300sc584IggmusPk GM78 p300 IgM p300_(SC-584) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001813 1813 GSM935559 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878P300sc584IggmusPk None Peaks Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 p300 SC584 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878P300IggmusPk GM78 p300 IgM p300 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002824 2824 GSM935294 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878P300IggmusPk None Peaks EP300(c-20) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 p300 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Nrf1IggmusPk GM78 Nrf1 IgM Nrf1 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-19 2011-10-19 wgEncodeEH001846 1846 GSM935309 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Nrf1IggmusPk None Peaks NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Nrf1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878NfybIggmusPk GM78 NYB IgM NF-YB GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002065 2065 GSM935507 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878NfybIggmusPk None Peaks NFYB is the beta subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment GM12878 NF-YB IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878NfyaIggmusPk GM78 NYA IgM NF-YA GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002064 2064 GSM935506 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878NfyaIggmusPk None Peaks NFYA is the alpha subunit of the trimeric NFY transcription factor complex that binds to the ubiquitous CCAAT motif B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment GM12878 NF-YA IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878NfkbTnfaIggrabPk GM78 TNF NKB IgR NFKB GM12878 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000690 690 GSM935478 Snyder Stanford hg18 exp wgEncodeSydhTfbsGm12878NfkbTnfaIggrabPk TNFa Peaks Epitope mapping at the C-terminus of NF-kappa-B p65 of human origin, recommended for detection of NFKB p65 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University human recombinant TNF-alpha from eBioscience [product# 14-8329-62] (Snyder) Regions of enriched signal in experiment GM12878 NFKB IgG-rab TNFa ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Nfe2sc22827StdPk GM78 NFE2 Std NF-E2_(SC-22827) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2010-09-03 2011-06-03 wgEncodeEH001808 1808 GSM935652 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Nfe2sc22827StdPk None Peaks Transcription factor NFE2 45 kDa subunit is a component of the NFE2 complex and essential for regulating erythroid and megakaryocytic maturation and differentiation. Binds to the hypersensitive site 2 (HS2) of the beta-globin control region (LCR). This subunit (NFE2)recognizes the TCAT/C sequence of the AP-1-like core palindrome present in a number of erythroid and megakaryocytic gene promoters. Requires MAFK or other small MAF proteins for binding to the NFE2 motif. May play a role in all aspects of hemoglobin production from globin and heme synthesis to procurement of iron. NFE2 has been shown to interact with CREB binding protein. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 NF-E2 SC22827 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Mxi1IggmusPk GM78 Mxi1 IgM Mxi1_(AF4185) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002026 2026 GSM935431 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Mxi1IggmusPk None Peaks Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Mxi1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Mazab85725IggmusPk GM78 MAZ IgM MAZ_(ab85725) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002852 2852 GSM935283 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Mazab85725IggmusPk None Peaks May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 MAZ IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878MaxIggmusPk GM78 Max IgM Max GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002806 2806 GSM935518 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878MaxIggmusPk None Peaks The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 Max IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878MafkIggmusPk GM78 MafK IgM MafK_(ab50322) GM12878 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-06-30 2013-03-30 wgEncodeEH003361 3361 GSM1003616 Snyder Stanford exp wgEncodeSydhTfbsGm12878MafkIggmusPk None Peaks NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 MafK (ab50322) IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878JundStdPk GM78 JunD Std JunD GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000639 639 GSM935541 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878JundStdPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment GM12878 JunD Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878JundIggrabPk GM78 JunD IgR JunD GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEH003370 3370 GSM1003634 Snyder Stanford exp wgEncodeSydhTfbsGm12878JundIggrabPk None Peaks The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq) B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 JunD IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Irf3IggmusPk GM78 IRF3 IgM IRF3 GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-20 wgEncodeEH001809 1809 GSM935651 Snyder Stanford PeakSeq1.0.  Because of the common difficulty in achieving strong signal with the GM12878 cell line, we submit this dataset, although it narrowly misses the peak concordance standard. hg19 exp wgEncodeSydhTfbsGm12878Irf3IggmusPk None Peaks Mediates interferon-stimulated response element (ISRE) promoter activation. DsRNA leads to IRF3 phosphorylation on the C-terminal serine/threonine cluster. This induces a conformational change, leading to its dimerization, nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of genes under the control of ISRE. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 IRF3 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Ikzf1iknuclaStdPk GM78 IKZF1 Std IKZF1_(IkN)_(UCLA) GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2012-09-18 wgEncodeEH002811 2811 GSM935442 Snyder USC PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Ikzf1iknuclaStdPk None Peaks IKAROS family zinc finger 1 (Ikaros or IKZF1) is a C2H2 zinc finger transcription factor that is associated with various chromatin-modifying complexes and is suggested to play a role in the development of lymphocytes, B- and T-cells. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Farnham - University of Southern California Regions of enriched signal in experiment GM12878 IKZF1 IKN UCLA Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Gcn5StdPk GM78 GCN5 Std GCN5 GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-21 2011-10-20 wgEncodeEH001874 1874 GSM935415 Snyder Harvard PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Gcn5StdPk None Peaks KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4 B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Struhl - Harvard University Regions of enriched signal in experiment GM12878 GCN5 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878ErraIggrabPk GM78 ERRA IgR ERRA GM12878 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003387 3387 GSM1003605 Snyder Stanford exp wgEncodeSydhTfbsGm12878ErraIggrabPk None Peaks Epitope corresponding to amino acids 81-160 mapping near the N-terminus of ERRalpha of human origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 ERRA IgG-rab ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Elk112771IggmusPk GM78 ELK1 IgM ELK1_(1277-1) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEH002851 2851 GSM935345 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Elk112771IggmusPk None Peaks Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 ELK1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Ebf1sc137065StdPk GM78 EBF1 Std EBF1_(SC-137065) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001832 1832 GSM935375 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Ebf1sc137065StdPk None Peaks Early B-cell factor 1. Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 EBF1 Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878E2f4IggmusPk GM78 E2F4 IgM E2F4 GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEH002867 2867 GSM935330 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878E2f4IggmusPk None Peaks mapping at the C-terminus of E2F4 of human origin B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 E2F4 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdPk GM78 CTCF Std CTCF_(SC-15914) GM12878 std ChipSeq ENCODE Jan 2011 Freeze 2011-01-20 2011-10-19 wgEncodeEH001851 1851 GSM935611 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdPk None Peaks Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 CTCF Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Corestsc30189IggmusPk GM78 COREST IgM COREST_(sc-30189) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEH002841 2841 GSM935583 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Corestsc30189IggmusPk None Peaks Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 COREST SC30189 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Chd2ab68301IggmusPk GM78 CHD2 IgM CHD2_(AB68301) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001831 1831 GSM935378 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Chd2ab68301IggmusPk None Peaks CHD family of proteins are characterized by presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 CHD2 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Chd1a301218aIggmusPk GM78 CHD1 IgM CHD1_(A301-218A) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2012-02-04 2012-11-03 wgEncodeEH002823 2823 GSM935301 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Chd1a301218aIggmusPk None Peaks CHD1 is a member of the CHD (chromodomain-helicase-DNA-binding) family of proteins that interacts with nucleosomes and plays a role in chromatin remodeling to modulate transcription. The members of the CHD family of proteins possess 3 common structural and functional domains: a chromodomain (chromatin organization modifier), an SNF2-like helicase/ATPase domain, and a C-terminal DNA-binding domain. CHD1 has been shown to interact with the transcriptional corepressor NCoR and histone deacetylase 1 indicating a role in transcriptional regulation. CHD1 has also been shown to interact with the Paf1 complex and Rtf1 implicating an additional role in transcriptional elongation. Alternate names for CHD1 include chromodomain-helicase-DNA-binding protein 1, ATP-dependent helicase CHD1, and DKFZp686E2337. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 CHD1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878CfosStdPk GM78 cFOS Std c-Fos GM12878 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH000622 622 GSM935409 Snyder Yale hg18 exp wgEncodeSydhTfbsGm12878CfosStdPk None Peaks Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Yale University Regions of enriched signal in experiment GM12878 c-FOS Standard ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Cdpsc6327IggmusPk GM78 CDP IgM CDP_(sc-6327) GM12878 IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEH003386 3386 GSM1003604 Snyder Stanford PeakSeq1.0 exp wgEncodeSydhTfbsGm12878Cdpsc6327IggmusPk None Peaks CDP (for CCAAT displacement protein) was identified as a repressor for tran- scription of developmentally regulated genes. It is a homeodomain protein that appears to compete with transcriptional activating proteins for binding to the promoter regions of various genes. CDP contains three cut repeats which function as DNA binding domains. It has been demonstrated that cut repeat domains have the capacity to bind to DNA in conjunction with or independently of homeodomain DNA binding. CDP has been shown to be the DNA-binding subunit of the HiNF-D complex, which contains cyclin A, Cdc2 and an Rb-related protein in addition to CDP. Histone expression is required for the transition to S phase in the cell cycle. The HiNF-D complex regulates the transcription of Histone H4, H3 and H1 genes, allowing cells to progress from G1 to S phase. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 CDP (SC-6327) IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Brca1a300IggmusPk GM78 BRC1 IgM BRCA1_(A300-000A) GM12878 IgG-mus ChipSeq ENCODE Jan 2011 Freeze 2011-01-18 2011-10-18 wgEncodeEH001830 1830 GSM935377 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Brca1a300IggmusPk None Peaks Nuclear phosphoprotein that plays a role in maintaining genomic stability, and acts as a tumor suppressor. Associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. Plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 BRCA1 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeSydhTfbsGm12878Bhlhe40cIggmusPk GM78 BHL4 IgM BHLHE40_(NB100-1800) GM12878 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH002025 2025 GSM935430 Snyder Stanford PeakSeq1.0 hg19 exp wgEncodeSydhTfbsGm12878Bhlhe40cIggmusPk None Peaks This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Regions of enriched signal in experiment GM12878 BHLHE40 NB100 IgG-mus ChIP-seq Peaks from ENCODE/SYDH Regulation 
wgEncodeUchicagoTfbs UChicago TFBS GSE31363 Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago Regulation Description This track maps genome-wide human transcription factor binding sites using second-generation massively parallel sequencing. This mapping uses expressed transcription factors as GFP-tagged fusion proteins after bacterial artificial chromosome (BAC) recombineering (recombination-mediated genetic engineering). The University of Chicago and Max Planck Institute (Dresden) pipeline generates recombineered BACs for the production of cell lines or animals that express fusion proteins from epitope-tagged transgenes. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. For each cell type, this track contains the following views: Peaks Regions of signal enrichment based on processed data (usually normalized data from pooled replicates). Signal Density graph (wiggle) of signal enrichment based on aligned read density. Peaks and signals displayed in this track are the results of pooled replicate sequence. Alignment files for each replicate are available for download. Methods Cells were grown according to the approved ENCODE cell culture protocols. Recombineering Strategy To facilitate high-throughput production of the transgenic constructs, the program BACFinder (Crowe et al., 2002) automatically selects the most suitable BAC clone for any given human gene and generates the sets of PCR primers required for tagging and verification (Poser et al., 2008). Recombineering is used for tagging cassettes at either the N or C terminus of the protein. The N-terminal cassette has a dual eukaryotic-prokaryotic promoter (PGK-gb2) driving a neomycin-kanamycin resistance gene within an artificial intron inside the tag coding sequence. The selection cassette is flanked by two loxP sites and can be permanently removed by Cre Recombinase-mediated excision. The C-terminal cassette contains the sequence encoding the tag followed by an internal ribosome entry site (IRES) in front of the neomycin resistance gene. In addition, a short bacterial promoter (Gb3) drives the expression of the neomycin-kanamycin resistance gene in E. coli. The tagging cassettes, containing 50 nucleotides of PCR-introduced homology arms, were inserted into the BAC by recombineering, either behind the start codon (for the N-terminal tag) or in front of the stop codon (for the C-terminal tag) of the gene. E. coli cells that had successfully recombined the cassette were selected for kanamycin resistance in liquid culture. Each saturated culture from a specific recombineering reaction derived 10-200 independent recombination events. Two independent clones were checked for each PCR through the tag insertion point and 97% (85/88) yielded a PCR product of the expected size. Most of the clones that failed to grow were missing the targeted genomic region. An estimated 10% of the BACs used were chimeric, rearranged or wrongly mapped. Thus, initial results indicated that the necessary recombineering steps could be carried out with high fidelity. The White lab produced all epitope tagged transcription and chromatin factor BACs, as well as the genome-wide ChIP data and analysis. An application of this approach to the analysis of closely related paralogs (RARa and RARg) yielded transcription factors, chromatin factors, cell lines, ChIP-chip data and ChIP-seq data (Hua et al., 2009). Such paralogous transcription factors often cannot otherwise be distinguished by antibodies. Sample Preparation ChIP DNA from samples were sheared to approximately 800 bp using a nebulizer. The ends of the DNA were polished and two unique adapters were ligated to the fragments. Ligated fragments of 150-200 bp were isolated by gel extraction and amplified using limited cycles of PCR. Sequencing System Illumina GAIIx and HySeq next-generation sequencing were used to produce all ChIP-seq data. Processing and Analysis Software Raw sequencing reads were aligned using Bowtie 0.12.5 (Langmead et al., 2009). The &quot;-m 1&quot; parameter was applied to suppress alignments mapping more than once in the genome. Reads were aligned to the UCSC hg19 assembly. Wiggle format signal files were generated with SPP 2.7.1 (Kharchenko et al., 2008) for R 2.7.1. MACS 1.3.7 was used to call peaks. The MACS parameters used varied by experiment. The White lab used goat anti-GFP antibody to perform ChIP in untagged K562 cells as a background control. The test IP was performed in the same manner as the background control. Results were expressed as values of the test normalized to the background. Credits These data and annotations were created by a collaboration of University of Chicago and Argonne National Laboratory: Kevin White (Principal Investigator at University of Chicago) Subhradip Karmakar (Project Lead at University of Chicago) Nick Bild (Data Analyst at University of Chicago) Alina Choudhury (Laboratory Technician at University of Chicago) Marc Domanus (Sequencing Technician at Argonne National Lab) References Crowe ML, Rana D, Fraser F, Bancroft I, Trick M. BACFinder: genomic localisation of large insert genomic clones based on restriction fingerprinting. Nucleic Acids Res. 2002 Nov 1;30(21):e118. Hua S, Kittler R, White KP. Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell. 2009 Jun 26;137(7):1259-71. Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008 Dec;26(12):1351-9. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Poser I, Sarov M, Hutchins JR, H&#233;rich&#233; JK, Toyoda Y, Pozniakovsky A, Weigl D, Nitzsche A, Hegemann B, Bird AW et al. BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods. 2008 May;5(5):409-15. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUchicagoTfbsViewSignal Signal Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562Enr4a1ControlSig K562 NR4A1/GFP Sg eGFP-NR4A1 K562 Control_eGFP-NR4A1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001212 1212 GSM777637 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562Enr4a1ControlSig Signal NR4A1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-NR4A1 Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Signal K562 NR4A1 GFP-tag TFBS Signal from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562EjundControlSig K562 JunD/GFP Sg eGFP-JunD K562 Control_eGFP-JunD ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001211 1211 GSM777639 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562EjundControlSig Signal JUND leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-JUND Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Signal K562 JunD GFP-tag TFBS Signal from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562EjunbControlSig K562 JunB/GFP Sg eGFP-JunB K562 Control_eGFP-JunB ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001210 1210 GSM777638 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562EjunbControlSig Signal JUNB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-JunB Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Signal K562 JunB GFP-tag TFBS Signal from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562Ehdac8ControlSig K562 HDAC8/GFP Sg eGFP-HDAC8 K562 Control_eGFP-HDAC8 ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001209 1209 GSM777640 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562Ehdac8ControlSig Signal HDAC8 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-HDAC8 Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Signal K562 HDAC8 GFP-tag TFBS Signal from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562Egata2ControlSig K562 GATA2/GFP Sg eGFP-GATA2 K562 Control_eGFP-GATA2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001208 1208 GSM777641 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562Egata2ControlSig Signal GATA2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-GATA2 Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Signal K562 GATA2 GFP-tag TFBS Signal from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562EfosControlSig K562 FOS/GFP Sg eGFP-FOS K562 Control_eGFP-FOS ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001207 1207 GSM777644 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562EfosControlSig Signal FOS leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-FOS Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Signal K562 FOS GFP-tag TFBS Signal from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsPeaks Peaks Transcription Factor Binding Sites by Epitope-Tag from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562Enr4a1ControlPk K562 NR4A1/GFP Pk eGFP-NR4A1 K562 Control_eGFP-NR4A1 ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001212 1212 GSM777637 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562Enr4a1ControlPk Peaks NR4A1 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-NR4A1 Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Regions of enriched signal in experiment K562 NR4A1 GFP-tag TFBS Peaks from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562EjundControlPk K562 JunD/GFP Pk eGFP-JunD K562 Control_eGFP-JunD ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001211 1211 GSM777639 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562EjundControlPk Peaks JUND leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-JUND Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Regions of enriched signal in experiment K562 JunD GFP-tag TFBS Peaks from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562EjunbControlPk K562 JunB/GFP Pk eGFP-JunB K562 Control_eGFP-JunB ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001210 1210 GSM777638 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562EjunbControlPk Peaks JUNB leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-JunB Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Regions of enriched signal in experiment K562 JunB GFP-tag TFBS Peaks from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562Ehdac8ControlPk K562 HDAC8/GFP Pk eGFP-HDAC8 K562 Control_eGFP-HDAC8 ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001209 1209 GSM777640 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562Ehdac8ControlPk Peaks HDAC8 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-HDAC8 Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Regions of enriched signal in experiment K562 HDAC8 GFP-tag TFBS Peaks from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562Egata2ControlPk K562 GATA2/GFP Pk eGFP-GATA2 K562 Control_eGFP-GATA2 ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001208 1208 GSM777641 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562Egata2ControlPk Peaks GATA2 leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-GATA2 Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Regions of enriched signal in experiment K562 GATA2 GFP-tag TFBS Peaks from ENCODE/UChicago Regulation 
wgEncodeUchicagoTfbsK562EfosControlPk K562 FOS/GFP Pk eGFP-FOS K562 Control_eGFP-FOS ChipSeq ENCODE Jan 2011 Freeze 2011-01-27 2011-10-27 wgEncodeEH001207 1207 GSM777644 White UChicago Illumina_GA2 exp wgEncodeUchicagoTfbsK562EfosControlPk Peaks FOS leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC This data represents a control being compared to experiments using antibody eGFP-FOS Chromatin IP Sequencing White White - University of Chicago Illumina Genome Analyzer II Regions of enriched signal in experiment K562 FOS GFP-tag TFBS Peaks from ENCODE/UChicago Regulation 
wgEncodeUmassDekker5C UMass 5C GSE39510 Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass. Regulation Description This track contains chromatin interaction data generated using the 5C (Chromatin Conformation Capture Carbon Copy) method by the ENCODE group (Dekker Lab) located at the University of Massachusetts, Worcester, MA. This track shows the significant looping interactions between transcriptional start sites (TSS) and distal regulatory elements in the context of the 44 ENCODE pilot regions spanning 1% of the human genome. Although the DNA is a linear sequence, the chromatin, which is packed and organized inside the nucleus, does not function linearly. This is most clearly illustrated by the fact that genes are often regulated by elements that are located hundreds of kilobases away in the linear genome. Imaging techniques have shown that regulatory elements can act over large genomic distances by engaging in direct physical interactions with target genes, resulting in the formation of chromatin loops. Based on these observations, we have envisaged that the spatial organization of the genome resembles a three-dimensional network that is driven by physical associations between genes and regulatory elements, both in cis (within the same chromosome) and in trans (between different chromosomes) (Dekker, 2006). Apart from imaging technology which is labor intensive and low-throughput, long-range chromatin looping interactions can be detected using the Chromosome Conformation Capture (3C) technology (Dekker et al., 2002). The 3C method employs formaldehyde cross-linking to covalently link interacting chromatin segments in intact cells. Cells are subsequently lysed and chromatin is digested with a restriction enzyme of choice. The digested fragments are then ligated under dilute conditions to facilitate intramolecular ligation. The result is a genome-wide interaction library of ligation products corresponding to all possible chromatin interactions. Specific ligation products can then be detected by PCR using specific primer pairs. The 5C method was developed to dramatically increase 3C throughput (Dostie et al., 2006; Dostie and Dekker, 2007). The 5C method greatly increases the scale of chromatin interaction detection by replacing the PCR detection step of 3C with ligation-mediated amplification (LMA). LMA is advantageous due to a much higher level of multiplexing by using thousands of primers in a single reaction to detect millions of chromatin interactions (ligation junctions) in parallel. The LMA step effectively "copies" 3C ligation products into much smaller 5C ligation products that precisely correspond to ligation junctions formed during the 3C procedure. The products of the multiplexed LMA reaction constitute the 5C library. The composition of the 5C library is determined using high-throughput DNA sequencing. Display Conventions and Configuration In the graphical display, the significant looping interactions in cis (i.e., from the same ENCODE pilot regions) are represented by blocks and connected by a horizontal line. Users can opt to filter the significant looping interactions according to their respective z-score (scaled to 0-1000) by using the built-in genome browser display score threshold. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. File Conventions The following types of data are available for download: Matrix Interaction files are in a matrix format indicating interaction strength with "reverse primer name | genome version | reverse HindIII fragment coordinates" in the top row and "forward primer name | genome version | forward primer fragment coordinates" in the first column. The number of sequences mapped to each interaction fills the matrix. In order to understand the Matrix data, you must download the associated primer data file. Primer Primer data files include the sequences of the primers used in the experiments. These files are available for download in the supplemental materials. Raw Data Sequencing files provided in fastQ format. Methods The aim of the pilot study was to generate a "connectivity map" between transcription start sites (TSS) and distal regulatory elements within the 44 ENCODE PILOT regions. In the current scheme, 5C primers were designed for all HindIII restriction fragments. Reverse primers were designed on fragments containing the TSS of annotated genes. Forward primers were designed on all other fragments. This design allowed for the interrogation of all TSS with all other restriction fragments, thus generating an interaction map between TSS and regulatory elements. For gene desert ENCODE pilot regions (for example ENr313), an altered scheme of forward and reverse primers was designed. Primers were selected for relative uniqueness using a custom 15-mer frequency table and BLAST. A custom hexamer barcode was added to each primer to ensure the sequence was unique relative to the primer pool being used. Primers were also selected for the appropriate melting temperature and GC-content and a universal tail sequence for amplification. The 44 ENCODE regions were analyzed in two groups using two separate 5C primer pools. The first group (ENm) contained the manually-picked ENCODE regions, ENm001-014 and ENr313. The second group (ENr) contained the 30 randomly-picked ENCODE regions. The two 5C primer pools were made by pooling 5C primers for interrogating long-range interactions in the two groups of ENCODE regions. The primer pool for the ENm group contained a total of 3,150 primers (476 reverse 5C primers and 2674 forward 5C primers). This primer pool allowed interrogation of a total of 1,272,824 interactions. Of these, 83,427 interactions were between fragments that were both located in the same ENCODE region. This primer pool for the ENr group contained a total of 3,152 primers (505 reverse 5C primers and 2647 forward 5C primers). This primer pool allowed interrogation of a total of 1,336,735 interactions. Of these, 34,859 interactions were between fragments that were both located in the same ENCODE region. In total, 981 reverse primers and 5,321 forward primers were designed (corresponding to ~77.1% (6,302/8,174) of all HindIII fragments in the 44 ENCODE regions). Currently, data for two biological replicates have been generated for ENCODE Tier I (GM12878 and K562), Tier II (HeLa-S3), and H1 human embryonic stem cells (H1-hESC), spanning 14 ENCODE manual regions along with one random region (ENr313) as well as 30 random regions separately using high-throughput paired-end sequencing in the Illumina GA2 platform. The looping interactions, which are detected in both the biological replicates, are considered significant. Release Notes This is Release 2 (July 2012). There is no new data for this release all new data has the version number appended to the name (e.g., V2). Peak files have been reanalyzed and more complete Raw Data files have been submitted. Credits All provided data were produced by the Dekker Lab at UMass Medical School, Worcester, MA. The following personnel contributed to the project (contacts): Wet Lab: Amartya Sanyal Dry Lab: Bryan R. Lajoie, Gaurav Jain Principal Investigator: Job Dekker Additional information and/or vizualization tools can be found on the Dekker Lab website. References Ba&#249; D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA. The three-dimensional folding of the &#945;-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol. 2011 Jan;18(1):107-14. Dekker J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat. Methods. 2006;3(1):17-21. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002 Feb 15;295(5558):1306-11. Dostie J, Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nature Protocols. 2007;2(4):988-1002. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 Oct;16(10):1299-309. Lajoie BR, van Berkum NL, Sanyal A, Dekker J. My5C: web tools for chromosome conformation capture studies. Nat. Methods. 2009;6(1):690-91. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUmassDekker5CHelas3PkV2 HeLa-S3 Pk HeLa-S3 5C ENCODE Jul 2012 Freeze 2012-06-05 2011-01-25 2011-10-25 wgEncodeEH001667 1667 GSM970497 Dekker UMass-Dekker wgEncodeUmassDekker5CHelas3PkV2 Peaks cervical carcinoma 5C Chromatin Interactions Dekker Dekker - University of Massachusettes Regions of enriched signal in experiment HeLa-S3 5C Peaks from ENCODE/UMass-Dekker Regulation 
wgEncodeUmassDekker5CK562PkV2 K562 Pk K562 5C ENCODE Jul 2012 Freeze 2012-06-05 2011-01-25 2011-10-25 wgEncodeEH001668 1668 GSM970500 Dekker UMass-Dekker wgEncodeUmassDekker5CK562PkV2 Peaks leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC 5C Chromatin Interactions Dekker Dekker - University of Massachusettes Regions of enriched signal in experiment K562 5C Peaks from ENCODE/UMass-Dekker Regulation 
wgEncodeUmassDekker5CH1hescPkV2 H1-hESC Pk H1-hESC 5C ENCODE Jul 2012 Freeze 2012-06-05 2011-01-25 2011-10-25 wgEncodeEH001666 1666 GSM970498 Dekker UMass-Dekker wgEncodeUmassDekker5CH1hescPkV2 Peaks embryonic stem cells 5C Chromatin Interactions Dekker Dekker - University of Massachusettes Regions of enriched signal in experiment H1-hESC 5C Peaks from ENCODE/UMass-Dekker Regulation 
wgEncodeUmassDekker5CGm12878PkV2 GM12878 Pk GM12878 5C ENCODE Jul 2012 Freeze 2012-06-05 2011-01-25 2011-10-25 wgEncodeEH001665 1665 GSM970499 Dekker UMass-Dekker wgEncodeUmassDekker5CGm12878PkV2 Peaks B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus 5C Chromatin Interactions Dekker Dekker - University of Massachusettes Regions of enriched signal in experiment GM12878 5C Peaks from ENCODE/UMass-Dekker Regulation 
wgEncodeUncBsuProtGenc UNC/BSU ProtGenc Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ. Expression Description The ENCODE project has revealed the functional elements of segments of the human genome in unprecedented detail. However, the ability to distinguish between transcripts designated for translation into protein and those that serve purely regulatory roles remains elusive. A standard means to determine if translation is occurring is to measure protein produced by transcripts via mass spectrometry-based proteogenomic mapping. In this process, proteins were digested to peptides using a protease such as trypsin and these petides were chromatographically fractionated and fed into a tandem mass spectrometer (MS/MS). This process creates a signature series of fragment masses which can be scanned against the theoretical translation and proteolytic digest of an entire genome to identify the genomic origins of sample proteins (Giddings et al., 2003). This proteogenomic track displays mass spectrometry data that have been matched to genomic sequences for selected cell lines, using a workflow and software specifically designed for this purpose. The track can be used to identify which parts of the genome are translated into proteins, to verify which transcripts discovered by other ENCODE experiments are protein-coding, to reveal new genes and/or splice variants and proteins with post-translational modifications (PTM). Of particular interest is the possibility of uncovering the translation of small open reading frames (ORFs), antisense transcripts, or protein-coding regions that have been annotated as introns previously. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Color differences among the views are arbitrary. They provide a visual cue for distinguishing between the different cell types and compartments. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. This track shows peptide mappings as contiguous rectangular items rendered in grayscale according to their score, with darker items representing higher-confidence peptide mappings. The name of each item is the amino acid sequence of the peptide where a period (.) at the end of a name signifies a stop codon. Peptide Genome and GENCODE Mapping(Filtered) Peptide mapping results based on hg19 and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered for a false discovery rate (FDR) better than 5%. Specific field descriptions can be found below. Modified Peptide Genome and GENCODE Mapping(Filtered) Modified peptide mapping results based on hg19 and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered for a false discovery rate (FDR) better than 5%. Unfiltered views are available on the Downloads page. Fields specific to Proteogenomic tracks include: The Item names the peptide sequence and is appended with a number for proteins with post-translational modifications (PTM) representing the integer portion of the PTM mass. The peptide sequence appears as a short label beside the main Genome Browser display window depending on the view configuration. The Score is used to render shade to displayed rectangular items and is derived from the rawScore (see below) given by the proteomics peptide mapping software Peppy. It is computed as [(rawScore - rawScore at 10% FDR cutoff) / (rawScore at near 0% FDR cutoff - rawScore at 10% FDR cutoff)] * 1000, and is then converted to an integer. Raw scores above the 0% FDR threshold have a score of 1000 (best), while those below the 10% FDR threshold have a score of 0 (worst). The rawScore is given by Peppy and is expressed as the negative log 10 of the p-value, which reflects the confidence of the mapping between the peptides and the spectrums. On the item details pages, rawScore is labeled: Raw score for a peptide/spectrum match. The spectrumId is an identifier of the spectrum associated with the peptide mapping and can be used to track the original spectrum. On the item details pages, spectrumId is labeled: An identifier of the spectrum associated with the peptide mapping. The peptideRank is a rank of the peptide/spectrum match used for a spectrum matching to different peptides. A spectrum can be chimeric (containing more than one peptide) and the spectrum can be mapped to two or more distinct peptides. Here, only the top-scoring match is reported. If more than one peptide "tied" for the top score, then all peptides were included and all matches have a peptideRank of 1. On the item details pages, peptideRank is labeled: Rank of the peptide/spectrum match, for spectrum matching to different peptides. The peptideRepeatCount indicates the number of places in the genome where the peptide is encoded for a peptide/spectrum match. It reflects the prevalence or uniqueness of the peptide mapping in the genome. Those peptides mapped to only a few genomic locations will have a low peptideRepeatCount, whereas those peptides mapped to highly duplicated regions will have a high peptideRepeatCount. Peptides with a peptideRepeatCount greater than 10 times in the genome were deleted from the track (this field is for regular peptides only). On the item details pages, peptideRepeatCount is labeled: Indicates the number of places in the genome where the peptide is encoded for a peptide/spectrum match. The modificationMass reflects the additional molecular weight for each modified peptide matched to a spectrum (this field is for PTM peptides only). On the item details pages, modificationMass is labeled: Reflects the additional molecular weight for each modified peptide matched to a spectrum. Methods ENCODE cell lines K562, GM12878, H1-hESC and H1-neurons were used for this large scale proteomic analysis. Cell lines were cultured according to standard ENCODE cell culture protocols and tryptic peptides were prepared using In-gel digestion (Shevchenko et al., 2007), FASP (Wiseniewski et al., 2009; Manza et al., 2005) or MudPIT (Washburn et al., 2001) protocols as indicated for each sample. Tandem mass spectrometry (RPLC-MS/MS) analysis was then performed on an Eksigent Ultra-LTQ Orbitrap system or a Q Exactive system (Thermo Scientific) as indicated.* The number of arginine or lysine sites missed by the trypsin enzyme is indicated by the metadata parameter miscleavages. We performed proteogenomic mapping (Jaffe et al., 2004) on an in silico translation and proteolytic digestion of the whole human genome (UCSC Hg19), and the GENCODE translation of protein-coding transcripts database with up to one missed cleavage using Peppy software. The GENCODE version for H1-hESC (FASP protocol), K562, and GM12878 is V11 and it is V10 for H1-hESC (MudPIT protocol) and H1-neurons datasets. GENCODE V11 was initially used for database search and it was later found that GENCODE V10 is the preferred version and was subsequently used to replace GENCODE V11 for the analyses of the later datasets. Peppy's embedded algorithm matches the MS/MS spectra to peptides and outputs a matching score, and the peptides are then mapped back to their corresponding genomic sequences. The peptide/spectrum matches (PSMs) found from Hg19 genome and GENCODE searches were compared and the PSMs of higher score from either matches were reported. If the scores from both matches are equal, both of them were reported. Additional peptides matches were found by GENCODE search that were not found in Hg19 genome search, some of which span slice junctions. Overall, a cross-comparison and inclusion of results from both database searches resulted in a greater coverage. For both the Hg19 genome and GENCODE database searches, a blind search for post-translational modifications (PTMs) was performed using Peppy software. In a blind PTM search, when Peppy matches a MS/MS spectrum to a peptide, if the matching score is increased after the addition of the molecular weight (MW) of a potential PTM, the peptide is determined as having a PTM. In the output of both the Hg19 genome and GENCODE searches, some spectra were output as matched with peptides of PTMs and others were output as matched with regular peptides, i.e., peptides without PTMs. Once the best-ranking PSMs were identified from either search, the regular peptides and peptides with PTMs were displayed in separate tracks. For each data set, a reverse database search was also performed using all spectra to calculate the false discovery rate (FDR) (Elias et al., 2007). Only those matches with a FDR rate below 5% were included in this track. The unfiltered results of those peptides matches with an FDR rate below 10% are available for download. *H1-hESC (FASP protocol), K562 and GM12878 samples were analyzed on the Eksigent Ultra LTQ Orbitrap system (Thermo Scientific) whereas H1-hESC (MudPIT protocol), H1-neurons sample were analyzed on the Q Exactive system (Thermo Scientific). Release Notes This is Release 1 of this track (Sept 2012). Unlike other ENCODE data, these data are not archived at GEO but at Proteome Commons. The first 32 digits of the Tranche Hash for each data set is stored as the labExpId. Credits Proteogenomic mapping: Dr. John Wrobel, Dr. Jainab Khatun, Mr. Brian Risk, and Mr. David Thomas (Giddings Lab). Proteomic analysis: Dr. Yanbao Yu, Dr. Harsha Gunawardena, Dr. Ling Xie and Ms. Li Wang (Chen Lab). Main Contact: John Wrobel References Giddings MC, Shah AA, Gesteland R, Moore B. Genome-based peptide fingerprint scanning. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):20-5. Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc. 2006;1(6):2856-60. Wisniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods. 2009 May;6(5):359-62. Manza LL, Stamer SL, Ham AJ, Codreanu SG, Liebler DC. Sample preparation and digestion for proteomic analyses using spin filters. Proteomics. 2005 May;5(7):1742-5. Washburn MP, Wolters D, Yates JR 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 2001 Mar;19(3):242-7. Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics. 2004 Jan;4(1):59-77. Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods. 2007 Mar;4(3):207-14. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column above. The full data release policy for ENCODE is available here. 
wgEncodeProtGenoSuper ENC ProtGeno ENCODE Proteogenomics Expression Description This super track shows proteogenomic mappings of peptides from ENCODE cell types mapped to the human genome which represent fragments of translated proteins from the respective cell lines. Proteogenomic methods differ from conventional mass-spec proteomic methods. Conventional mass-spec proteomic methods identify peptides by comparing them to peptides produced from known proteins. In contrast, proteogenomic methods compare the peptides to all peptides that might theoretically be produced by the six possible translation frames of the genome (three on the forward strand plus three on the reverse strand) to identify the genomic region from which the peptides were produced. Study of proteogenomic data offers insights on numerous regulatory mechanisms, including: translation, pre-mRNA splicing and transcript diversity, nonsense-mediated decay, and transcription of novel protein-coding genes. Two tracks UNC/BSU ProtGenc and UNC/BSU ProtGeno that differ in database search scheme are presented here. UNC/BSU ProtGenc are the combined results from searching against Hg19 and GENCODE of peptides of both regular and post-translational modifications. UNC/BSU ProtGeno only contains the database search results of Hg19 of regular peptides. Display Conventions and Configuration Most ENCODE tracks contain multiple subtracks corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages. Credits These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks. References Giddings MC, Shah AA, Gesteland R, Moore B. Genome-based peptide fingerprint scanning. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):20-5. Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics. 2004 Jan;4(1):59-77. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeUncBsuProtGencViewpepMapGcFt pepMapping Gc Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ. Expression 
wgEncodeUncBsuProtGencK562CellIngelpepMapGcFt K562 Ce K562 Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003041 3041 Giddings UNC/BSU xcl9urKnTHhc0qEOIR+zbkKc4hlktYQx enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cell In-gel wgEncodeUncBsuProtGencK562CellIngelpepMapGcFt pepMapGcFt leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell In-gel digestion proteomics protocol (Giddings) Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. K562 In-gel ProtG GENCODE11 Hg19 Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencH1neuronsCellMudpitpepMapGcFt H1-neurons Ce H1-neurons Proteogenomics ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003043 3043 Giddings UNC/BSU AmpuUJeecTjp8adhqKVDfzos/0Q694X4 enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=50ppm cell MudPIT wgEncodeUncBsuProtGencH1neuronsCellMudpitpepMapGcFt pepMapGcFt neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell Multidimensional Protein Identification Technology (MudPIT) proteomics protocol (Giddings) Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. H1-neurons MudPIT ProtG GENCODE10 Hg19 Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencH1hescCellMudpitpepMapGcFt H1-hESC Ce M H1-hESC Proteogenomics ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003042 3042 Giddings UNC/BSU Qe8pClnCCX+8LPbKv7RuRfN/rXkxbq5G enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=50ppm cell MudPIT wgEncodeUncBsuProtGencH1hescCellMudpitpepMapGcFt pepMapGcFt embryonic stem cells Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell Multidimensional Protein Identification Technology (MudPIT) proteomics protocol (Giddings) Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. H1-hESC MudPIT ProtG GENCODE10 Hg19 Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencH1hescCellFasppepMapGcFt H1-hESC Ce F H1-hESC Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003040 3040 Giddings UNC/BSU YvRPXIoQz2jxniZvFp68FrcHhobcfvAk enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cell FASP wgEncodeUncBsuProtGencH1hescCellFasppepMapGcFt pepMapGcFt embryonic stem cells Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell Filter-Assisted Sample Preparation (FASP) proteomics protocol (Giddings) Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. H1-hESC FASP ProtG GENCODE11 Hg19 Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencGm12878CytosolIngelpepMapGcFt GM12878 Cyt GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003039 3039 Giddings UNC/BSU g9xv8oYkcWO3eKO5h58XMTgCfe/5JTg8 enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cytosol In-gel wgEncodeUncBsuProtGencGm12878CytosolIngelpepMapGcFt pepMapGcFt B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University The fluid between the cells outer membrane and the nucleus In-gel digestion proteomics protocol (Giddings) Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. GM12878 Cytosol InGel ProtG GENCODE11 Hg19 Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencGm12878CellIngelpepMapGcFt GM12878 Ce GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003038 3038 Giddings UNC/BSU mmsilk35SUJQSp8Cls/3c42WCVEPxAcE enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cell In-gel wgEncodeUncBsuProtGencGm12878CellIngelpepMapGcFt pepMapGcFt B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell In-gel digestion proteomics protocol (Giddings) Peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. GM12878 In-gel ProtG GENCODE11 Hg19 Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencViewmPepMapGcFt modPepMapping Gc Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ. Expression 
wgEncodeUncBsuProtGencK562CellIngelmPepMapGcFt K562 Ce PTM K562 Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003041 3041 Giddings UNC/BSU xcl9urKnTHhc0qEOIR+zbkKc4hlktYQx enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cell In-gel wgEncodeUncBsuProtGencK562CellIngelmPepMapGcFt mPepMapGcFt leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell In-gel digestion proteomics protocol (Giddings) Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. K562 In-gel ProtG GENCODE11 Hg19 PTM Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencH1neuronsCellMudpitmPepMapGcFt H1-neurons Ce PTM H1-neurons Proteogenomics ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003043 3043 Giddings UNC/BSU AmpuUJeecTjp8adhqKVDfzos/0Q694X4 enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=50ppm cell MudPIT wgEncodeUncBsuProtGencH1neuronsCellMudpitmPepMapGcFt mPepMapGcFt neurons derived from H1 embryonic stem cells, newly promoted to tier 2: not in 2011 analysis Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell Multidimensional Protein Identification Technology (MudPIT) proteomics protocol (Giddings) Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. H1-neurons MudPIT ProtG GENCODE10 Hg19 PTM Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencH1hescCellMudpitmPepMapGcFt H1-hESC Ce M PTM H1-hESC Proteogenomics ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEH003042 3042 Giddings UNC/BSU Qe8pClnCCX+8LPbKv7RuRfN/rXkxbq5G enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=50ppm cell MudPIT wgEncodeUncBsuProtGencH1hescCellMudpitmPepMapGcFt mPepMapGcFt embryonic stem cells Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell Multidimensional Protein Identification Technology (MudPIT) proteomics protocol (Giddings) Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. H1-hESC MudPIT ProtG GENCODE10 Hg19 PTM Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencH1hescCellFaspmPepMapGcFt H1-hESC Ce PTM H1-hESC Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003040 3040 Giddings UNC/BSU YvRPXIoQz2jxniZvFp68FrcHhobcfvAk enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cell FASP wgEncodeUncBsuProtGencH1hescCellFaspmPepMapGcFt mPepMapGcFt embryonic stem cells Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell Filter-Assisted Sample Preparation (FASP) proteomics protocol (Giddings) Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. H1-hESC FASP ProtG GENCODE11 Hg19 PTM Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencGm12878CytosolIngelmPepMapGcFt GM12878 Cyt PTM GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003039 3039 Giddings UNC/BSU g9xv8oYkcWO3eKO5h58XMTgCfe/5JTg8 enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cytosol In-gel wgEncodeUncBsuProtGencGm12878CytosolIngelmPepMapGcFt mPepMapGcFt B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University The fluid between the cells outer membrane and the nucleus In-gel digestion proteomics protocol (Giddings) Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. GM12878 Cytosol InGel ProtG GENCODE11 Hg19 PTM Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGencGm12878CellIngelmPepMapGcFt GM12878 Ce PTM GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEH003038 3038 Giddings UNC/BSU mmsilk35SUJQSp8Cls/3c42WCVEPxAcE enzyme=trypsin,miscleavages=1,precursorMassTolerance=20ppm,msMsMassTolerance=500ppm cell In-gel wgEncodeUncBsuProtGencGm12878CellIngelmPepMapGcFt mPepMapGcFt B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Whole cell In-gel digestion proteomics protocol (Giddings) Modified peptide mapping results based on the hg19 genome and GENCODE annotation for mass-spectrometry-based proteomics experiments filtered by false discovery rate (FDR) better than 5%. GM12878 In-gel ProtG GENCODE11 Hg19 PTM Mapping from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProt UNC/BSU ProtGeno Proteogenomics Hg19 Mapping from ENCODE/Univ. North Carolina/Boise State Univ. Expression Description The ENCODE project has revealed the functional elements of segments of the human genome in unprecedented detail. However, the ability to clearly distinguish transcripts designated for translation into protein versus those that serve purely regulatory roles remains elusive. The standard means for doing this is to measure the proteins, if any, that are produced by transcripts via mass spectrometry-based proteogenomic mapping. In this process, chromatographically fractionated peptides are fed into a tandem mass spectrometer (MS/MS). The series of fragment masses produced in MS/MS create a signature that can then be used to identify the peptide from a protein or DNA sequence database. For proteogenomic mapping, this identifying spectrum is mapped directly back to its most likely encoding locus on a genome sequence (Giddings, et al. 2003). This allows the direct verification of protein-encoding transcripts. The proteogenomic track displays mass spectrometry data that have been matched to the genomic sequence for selected cell lines, using a workflow and software specifically designed for this purpose. The proteogenomic tracks can be used to identify which parts of the genome are translated into proteins, to verify which transcripts discovered by ENCODE are protein-encoding, and can also reveal new genes and/or splice variants of genes. Of particular interest may be its ability to reveal the translation of small open reading frames (ORFs), antisense transcripts, or sites annotated as introns that encode proteins. Display Conventions and Configuration The display for this track shows peptide mappings as contiguous, rectangular items. These items are rendered in grayscale according to the score, with darker items representing higher-confidence peptide mappings. The name of each item is the amino acid sequence of the peptide. If a period (.) appears at the end of a name, it signifies a stop codon. In addition to the displayed genomic coordinates, several additional fields are available for each track item. The Raw Score reflects the strength of the peptide mapping, in contrast to the Score field which reflects the confidence of the mapping. The Score field is computed as -100&times;log10(E-Value) for the peptide mapping, and scores of 200 or greater have an estimated 5% false discovery rate (FDR) while scores of 230 or greater have an estimated 1% FDR. The Raw Score offers an additional level of confidence: raw scores of 300 or greater have an estimated 5% false discovery rate. Note that Raw Score is not normalized for the length of the peptide mapping, while Score is. Consequently, short mappings might have a strong Raw Score but a weaker Score. The Spectrum ID is a semi-unique identifier of the spectrum associated with the peptide mapping, and can be used to track the origins of the mapping. The Peptide Rank indicates the rank of each peptide/spectrum mapping. A spectrum can be chimeric, containing more than one peptide, and the spectrum can be mapped with confidence to two or more distinct peptides. Peptides with ranks greater than 3 are deleted from the track. The Peptide Repeat Count indicates the number of places in the genome that match the peptide sequence. This reflects the uniqueness of the peptide mapping in the genome. Any mappings to highly-duplicated regions will have a high Peptide Repeat Count and peptides which were repeated more than 10 times in the genome were deleted from the track. Methods ENCODE cell lines K562 and GM12878 were used for large scale proteomic analysis. Cell lines were cultured according to standard ENCODE cell culture protocols and in-gel digestion was completed according to the standard protocol (Shevchenko, et al. 2007). The proteolytic enzyme trypsin was used to digest the proteins in order to produce short, MS/MS analyzable peptides. Trypsin is a common protease that typically cleaves proteins after Arginine or Lysine. The metadata parameter enzyme specifies the restriction enzyme used for digestion. Tandem mass spectrometry (RPLC-MS/MS) analysis was then performed on an Eksigent Ultra-LTQ Orbitrap system. However, due to enzyme inefficiency, it does not always cleave at Arginine or Lysine, so there may be peptides that include an uncleaved Arg/Lys site. The number of such missed cleavages allowed in the search is described by the metadata parameter miscleavages. We performed proteogenomic mapping (Jaffe, et al., 2004) with two missed cleavages allowed and using the whole human genomic sequence (UCSC hg19) via the genome fingerprint scanning (GFS) program (Giddings, et al. 2003) and newly developed Peppy (http://www.peppyresearch.com/). We used HMM_Score (Khatun, et al. 2008) to accurately match MS/MS spectra to their corresponding genome sequences. E-values are calculated, which estimate the number of results at the given score level which would be expected by random chance. We then empirically derived the false discovery rate for a given E-Value using a decoy database search and only those matches falling within the specified 5% FDR rate (E-Value &lt;0.01) are included in the track. The results with 10% FDR (E-Value &lt;0.05) are available under the Downloads page as Raw Signal. Release Notes This is Release 2 (July 2012). It contains a total of seven Proteogenomics experiments with the addition of one experiment available by download only. Unlike other ENCODE data, these data are not archived at GEO but at Proteome Commons. The first 32 digits of the Tranche Hash for each data set is stored as the labExpId. Credits Proteogenomic mapping: Dr. Jainab Khatun, Brian Risk, Mustaque Ahamed, Christopher Maier, Dr. John Wrobel and Dennis Crenshaw (Giddings Lab). Proteomic analysis: Drs. Yanbao Yu and Ling Xie (Chen Lab). Main Contact: Jainab Khatun References Giddings MC, Shah AA, Gesteland R, Moore B. Genome-based peptide fingerprint scanning. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):20-5. Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics. 2004 Jan;4(1):59-77. Khatun J, Hamlett E, Giddings MC. Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification. Bioinformatics. 2008 Mar 1;24(5):674-81. Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc. 2006;1(6):2856-60. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeUncBsuProtViewSignal Signal Proteogenomics Hg19 Mapping from ENCODE/Univ. North Carolina/Boise State Univ. Expression 
wgEncodeUncBsuProtK562NucleusSig K562 nucleus K562 Proteogenomics ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH001739 1739 Giddings UNC/BSU IIAwZ45L+6NW1WpXsldQPngd7uSYeRyG enzyme=trypsin,miscleavages=2,precursorMassTolerance=.1Da,msMsMassTolerance=0.5Da nucleus In-gel wgEncodeUncBsuProtK562NucleusSig Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA In-gel digestion proteomics protocol (Giddings) Signal K562 Nucleus Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtK562MitoSig K562 mitochondria K562 Proteogenomics ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH001738 1738 Giddings UNC/BSU Jpyz/zLWVrm2PiRJ9/xclTu3hL/xFr0A enzyme=trypsin,miscleavages=2,precursorMassTolerance=.1Da,msMsMassTolerance=0.5Da mitochondria In-gel wgEncodeUncBsuProtK562MitoSig Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Mitochondria In-gel digestion proteomics protocol (Giddings) Signal K562 Mitochondria Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtK562MembranefractionSig K562 membrane K562 Proteogenomics ENCODE Mar 2012 Freeze 2011-01-05 2012-10-05 wgEncodeEH001200 1200 Giddings UNC/BSU hdaLa/989p1R+esS5JtrPWNam6J6QDyK enzyme=trypsin,miscleavages=2,precursorMassTolerance=.1Da,msMsMassTolerance=0.5Da membraneFraction In-gel wgEncodeUncBsuProtK562MembranefractionSig Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University That fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes. In-gel digestion proteomics protocol (Giddings) Signal K562 Membrane Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtK562CytosolSig K562 cytosol K562 Proteogenomics ENCODE Mar 2012 Freeze 2011-06-03 2012-03-03 wgEncodeEH001737 1737 Giddings UNC/BSU Q8FP+m7/Ep+JBw6Sf0Y1ffd0L+rycBiQ enzyme=trypsin,miscleavages=2,precursorMassTolerance=.1Da,msMsMassTolerance=0.5Da cytosol In-gel wgEncodeUncBsuProtK562CytosolSig Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University The fluid between the cells outer membrane and the nucleus In-gel digestion proteomics protocol (Giddings) Signal K562 Cytosol Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGm12878NucleusSig GM12878 nucleus GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2011-01-05 2012-10-05 wgEncodeEH001199 1199 Giddings UNC/BSU V7YeoLFnPQLw3zGfK3PthRQUsPlna6Nj enzyme=trypsin,miscleavages=2,precursorMassTolerance=0.2Da,msMsMassTolerance=0.5Da nucleus In-gel wgEncodeUncBsuProtGm12878NucleusSig Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA In-gel digestion proteomics protocol (Giddings) Signal GM12878 Nucleus Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGm12878MitoSig GM12878 mito GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEH002074 2074 Giddings UNC/BSU ZOTAcOHHzELqE03RkiDdf8c+/4aLhjII enzyme=trypsin,miscleavages=2,precursorMassTolerance=0.1Da,msMsMassTolerance=0.5Da mitochondria In-gel wgEncodeUncBsuProtGm12878MitoSig Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University Mitochondria In-gel digestion proteomics protocol (Giddings) Signal GM12878 Mitochondria Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeUncBsuProtGm12878MembranefractionSig GM12878 membrane GM12878 Proteogenomics ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEH002073 2073 Giddings UNC/BSU OgqVm65vZlAv8IguaucWsujQnNWYC3vO enzyme=trypsin,miscleavages=2,precursorMassTolerance=0.1Da,msMsMassTolerance=0.5Da membraneFraction In-gel wgEncodeUncBsuProtGm12878MembranefractionSig Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Mass Spec Proteogenomic Mapping Giddings Giddings - University of North Carolina and Boise State University That fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes. In-gel digestion proteomics protocol (Giddings) Signal GM12878 Membrane Proteogenomic Hg19 Mapping Hits from ENCODE/UNC/BSU Expression 
wgEncodeOpenChromChip UTA TFBS GSE33213 None Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) Regulation Description These tracks display chromatin immunoprecipitation (ChIP-seq) evidence as part of the four Open Chromatin track sets (see below). ChIP-seq is a method to identify the specific location of proteins that are directly or indirectly bound to genomic DNA. By identifying the binding location of sequence-specific transcription factors, general transcription machinery components, and chromatin factors, ChIP can help in the functional annotation of the open chromatin regions identified by DNaseI HS mapping and FAIRE. Together with DNaseI HS and FAIRE experiments, these tracks display the locations of active regulatory elements identified as open chromatin in multiple cell types from the Duke, UNC-Chapel Hill, UT-Austin, and EBI ENCODE group. Within this project, open chromatin was identified using two independent and complementary methods: DNaseI hypersensitivity (HS) and Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE), combined with these ChIP-seq assays for select regulatory factors. DNaseI HS and FAIRE provide assay cross-validation with commonly identified regions delineating the highest confidence areas of open chromatin. These ChIP assays provide functional validation and preliminary annotation of a subset of open chromatin sites. Each method employed Illumina (formerly Solexa) sequencing by synthesis as the detection platform. The Tier 1 and Tier 2 cell types were additionally verified by a second platform, high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen. As a background control experiment, the input genomic DNA sample that was used for ChIP was sequenced. Crosslinked chromatin was sheared and the crosslinks were reversed without carrying out the immunoprecipitation step. This sample was otherwise processed in a manner identical to the ChIP sample as described below. The input track is useful in revealing potential artifacts arising from the sequence alignment process such as copy number differences between the reference genome and the sequenced samples, as well as regions of poor sequence alignability. For cell lines for which there is no input experiment available, the peaks were generated using the control of generic_male or generic_female, as an attempt to create a general background based on input data from several cell types. These files are in &quot;iff&quot; format, which is used when calling peaks with F-seq software, and can be downloaded from the production lab directly from under the section titled &quot;Copy number / karyotype correction.&quot; Other Open Chromatin track sets: Data for the DNaseI HS experiments can be found in Duke DNaseI HS. Data for the FAIRE experiments can be found in UNC FAIRE. A synthesis of all the open chromatin assays for select cell lines can be found in Open Chrom Synth. Display Conventions and Configuration This track is a multi-view composite track that contains a single data type with multiple levels of annotation (views). For each view, there are multiple subtracks representing different cell types that display individually on the browser. Instructions for configuring multi-view tracks are here. ChIP data displayed here represents a continuum of signal intensities. The Iyer lab recommends setting the &quot;Data view scaling: auto-scale&quot; option when viewing signal data in full mode to see the full dynamic range of the data. Note that in regions that do not have open chromatin sites, autoscale will rescale the data and inflate the background signal, making the regions appear noisy. Changing back to fixed scale will alleviate this issue. In general, for each experiment in each of the cell types, the UTA TFBS tracks contain the following views: Peaks Regions of enriched signal in ChIP experiments. Peaks were called based on signals created using F-Seq, a software program developed at Duke (Boyle et al., 2008b). Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant. The solid vertical line in the peak represents the point with highest signal. F-Seq Density Signal Density graph (wiggle) of signal enrichment calculated using F-Seq for the combined set of sequences from all replicates. F-Seq employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). This method does not look at fixed-length windows but rather weights contributions of nearby sequences in proportion to their distance from that base. It only considers sequences aligned 4 or less times in the genome and uses an alignability background model to try to correct for regions where sequences cannot be aligned. For each cell type, especially important for those with an abnormal karyotype, a model to try to correct for amplifications and deletions that is based on control input data was also used. Base Overlap Signal An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Peaks and signals displayed in this track are the results of pooled replicates. The raw sequence and alignment files for each replicate are available for download. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. To perform ChIP, proteins were cross-linked to DNA in vivo using 1&#37; formaldehyde solution (Bhinge et al., 2007; ENCODE Project Consortium, 2007). Cross-linked chromatin was sheared by sonication and immunoprecipitated using a specific antibody against the protein of interest. After reversal of the cross-links, the immunoprecipitated DNA was used to identify the genomic location of transcription factor binding. This was accomplished by sequencing of the ends of the immunoprecipitated DNA (ChIP-seq) using the Illumina (Solexa) sequencing system. ChIP data for Tier 1 and Tier 2 cell lines were verified by comparing multiple independent growths (replicates) and determining the reproducibility of the data. For some cell types, additional verification was performed using the same immunoprecipitated DNA by labeling and hybridizing to NimbleGen Human ENCODE tiling arrays (1&#37; of the genome) along with the input DNA as reference (ChIP-chip). A more detailed protocol is available here. DNA fragments isolated by ChIP are 100-200 bp in length, with the average length being 134 bp. Sequences from each experiment were aligned to the genome using Burrows-Wheeler Aligner (Li et al., 2010) for the GRCh37 (hg19) assembly. The command used for these alignments was: &gt; bwa aln -t 8 genome.fa s_1.sequence.txt.bfq &gt; s_1.sequence.txt.sai Where genome.fa is the whole genome sequence and s_1.sequence.txt.bfq is one lane of sequences converted into the required bfq format. Sequences from multiple lanes are combined for a single replicate using the bwa samse command, and converted in the sam/bam format using SAMtools. Only those that aligned to 4 or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes - see supplemental materials). The mappings of these short reads to the genome are available for download. The resulting digital signal was converted to a continuous wiggle track using F-Seq that employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Input data has been generated for several cell lines. These are used directly to create a control/background model used for F-Seq when generating signal annotations for these cell lines. These models are meant to correct for sequencing biases, alignment artifacts, and copy number changes in these cell lines. Input data is not being generated directly for other cell lines. Instead, a general background model was derived from the available input data sets. This should provide corrections for sequencing biases and alignment artifacts, but will not correct for cell type specific copy number changes. The exact command used for this step is: CTCF: &gt; fseq -l 300 -v -b &lt;bff files&gt; -p &lt;iff files&gt; aligments.bed c-Myc: &gt; fseq -l 600 -v -b &lt;bff files&gt; -p &lt;iff files&gt; aligments.bed PolII: &gt; fseq -l 800 -v -b &lt;bff files&gt; -p &lt;iff files&gt; aligments.bed Where the (bff files) are the background files based on alignability, the (iff files) are the background files based on the input experiments, and alignments.bed are a bed file of filtered sequence alignments. Discrete ChIP sites (peaks) were identified from ChIP-seq F-seq density signal. Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant. Data from the high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen were normalized using the Tukey biweight normalization, and peaks were called using ChIPOTle (Buck, et al., 2005) at multiple levels of significance. Regions matched on size to these peaks that were devoid of any significant signal were also created as a null model. These data were used for additional verification of Tier 1 and Tier 2 cell lines by ROC analysis. Files labeled Validation view containing this data are available for download. Release Notes Release 2 (August 2011) of this track adds 34 new experiments including 17 new cell lines. Enhancer and Insulator Functional assays: A subset of DNase and FAIRE regions were cloned into functional tissue culture reporter assays to test for enhancer and insulator activity. Coordinates and results from these experiments can be found here. Credits These data and annotations were created by a collaboration of multiple institutions (contact: Terry Furey) Duke University's Institute for Genome Sciences & Policy (IGSP): Alan Boyle, Lingyun Song, and Greg Crawford University of North Carolina at Chapel Hill: Paul Giresi, Jason Lieb and Terry Furey University of Texas at Austin: Zheng Liu, Ryan McDaniell, Bum-Kyu Lee, and Vishy Iyer European Bioinformatics Insitute: Paul Flicek, Damian Keefe, and Ewan Birney University of Cambridge, Department of Oncology and CR-UK Cambridge Research Institute (CRI) : Stefan Graf We thank NHGRI for ENCODE funding support. References Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res. 2007 Jun;17(6):910-6. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 2008 Jan 25;132(2):311-22. Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics. 2008 Nov 1;24(21):2537-8. Buck MJ, Nobel AB, Lieb JD. ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol. 2005;6(11):R97. Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods. 2006 Jul;3(7):503-9. Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006 Jan;16(1):123-31. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guig&#243; R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2007 Jun;17(6):877-85. Giresi PG, Lieb JD. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods. 2009 Jul;48(3):233-9. Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS et al. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res. 2012 Jan;22(1):9-24. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008 Nov;18(11):1851-8. Song L, Crawford GE. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5384. Publications Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS et al. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res. 2012 Jan;22(1):9-24. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here. 
wgEncodeOpenChromChipViewPeaks Peaks Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) Regulation 
wgEncodeOpenChromChipSpleenocCtcfPkRep1 Spleen CTCF Pk CTCF Spleen_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003464 3464 GSM1006883 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipSpleenocCtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen spleen tissue from NICHD donor IDs 1863 (Rep B1) and 4548 (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Spleen OC CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibPol2PkRep1 ProgFib Pol2 Pk Pol2 ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-10 2010-10-10 wgEncodeEH000606 606 GSM822282 Crawford UT-A privacy-noSequence p-value cutoff: 0.05 hg18 1 exp wgEncodeOpenChromChipProgfibPol2PkRep1 None Peaks RNA Polymerase II fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment ProgFib Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibCtcfPkRep1 ProgFib CTCF Pk CTCF ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-02 2010-10-02 wgEncodeEH000600 600 GSM822272 Crawford UT-A privacy-noSequence p-value cutoff: 0.05 hg18 1 exp wgEncodeOpenChromChipProgfibCtcfPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment ProgFib CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipPancreasocCtcfPkRep1 Pancreas CTCF Pk CTCF Pancreas_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003463 3463 GSM1006881 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipPancreasocCtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Pancreas OC CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipNhekCtcfPk NHEK CTCF Pk CTCF NHEK ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-30 2010-06-30 wgEncodeEH000559 559 GSM822271 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipNhekCtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment NHEK CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMedulloCtcfPkRep1 Medullo CTCF Pk CTCF Medullo ChipSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003440 3440 GSM1006893 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMedulloCtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Medullo CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLungocCtcfPkRep1 Lung CTCF Pk CTCF Lung_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003462 3462 GSM1006882 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipLungocCtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen lung tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase) and CF Center donor IDs DD006I (Rep B1 FAIRE) and DD007I (Rep B2 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Lung OC CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapCtcfAndroPkRep1 LNCaP CTCF Pk CTCF LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003460 3460 GSM1006887 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipLncapCtcfAndroPkRep1 androgen Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Regions of enriched signal in experiment LNCaP androgen CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapCtcfPkRep1 LNCaP CTCF Pk CTCF LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003459 3459 GSM1006874 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipLncapCtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment LNCaP CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipKidneyocCtcfPkRep1 Kidney CTCF Pk CTCF Kidney_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003461 3461 GSM1006886 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipKidneyocCtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Kidney OC CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm20000CtcfPkRep1 GM20000 CTCF Pk CTCF GM20000 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003458 3458 GSM1006873 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipGm20000CtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM20000 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19240CtcfPk GM19240 CTCF Pk CTCF GM19240 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-06 2010-07-06 wgEncodeEH000572 572 GSM822276 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm19240CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM19240 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19239CtcfPk GM19239 CTCF Pk CTCF GM19239 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000571 571 GSM822277 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm19239CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM19239 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19238CtcfPk GM19238 CTCF Pk CTCF GM19238 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000570 570 GSM822278 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm19238CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM19238 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13977CtcfPkRep1 GM13977 CTCF Pk CTCF GM13977 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003456 3456 GSM1006869 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipGm13977CtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM13977 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13976CtcfPkRep1 GM13976 CTCF Pk CTCF GM13976 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003448 3448 GSM1006885 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipGm13976CtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM13976 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12892CtcfPk GM12892 CTCF Pk CTCF GM12892 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-02 2010-07-02 wgEncodeEH000562 562 GSM822299 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm12892CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12892 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12891CtcfPk GM12891 CTCF Pk CTCF GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000569 569 GSM822294 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm12891CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12891 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10266CtcfPkRep1 GM10266 CTCF Pk CTCF GM10266 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003457 3457 GSM1006870 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipGm10266CtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM10266 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10248CtcfPkRep1 GM10248 CTCF Pk CTCF GM10248 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003446 3446 GSM1006891 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipGm10248CtcfPkRep1 Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM10248 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaPol2PkRep1 Gliobla Pol2 Pk Pol2 Gliobla ChipSeq ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001136 1136 GSM822302 Crawford UT-A p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipGlioblaPol2PkRep1 None Peaks RNA Polymerase II glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Gliobla Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaCtcfPkRep1 Gliobla CTCF Pk CTCF Gliobla ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-19 wgEncodeEH001135 1135 GSM822303 Crawford UT-A p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipGlioblaCtcfPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Gliobla CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipFibroblCtcfPkRep1 Fibrobl CTCF Pk CTCF Fibrobl ChipSeq ENCODE Jan 2011 Freeze 2010-10-13 2011-07-13 wgEncodeEH001127 1127 GSM822281 Crawford UT-A privacy-noSequence p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipFibroblCtcfPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. child fibroblast Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment Fibrobl CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2SerumstimPkRep1 MCF-7 Pol2 stm Pk Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003435 3435 GSM1006876 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMcf7Pol2SerumstimPkRep1 serum_stimulated_media Peaks RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Regions of enriched signal in experiment MCF-7 serum stim Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2SerumstvdPkRep1 MCF-7 Pol2 stv Pk Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEH003438 3438 GSM1006865 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMcf7Pol2SerumstvdPkRep1 serum_starved_media Peaks RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Regions of enriched signal in experiment MCF-7 serum starved Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2PkRep1 MCF-7 Pol2 Pk Pol2 MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001130 1130 GSM822295 Crawford UT-A p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipMcf7Pol2PkRep1 None Peaks RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment MCF-7 Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfVehPkRep1 MCF-7 veh CTCF Pk CTCF MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001132 1132 GSM822308 Crawford UT-A p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipMcf7CtcfVehPkRep1 vehicle Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) Regions of enriched signal in experiment MCF-7 vehicle CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSerumstimPkRep1 MCF-7 CTCF stm Pk CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003434 3434 GSM1006875 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMcf7CtcfSerumstimPkRep1 serum_stimulated_media Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Regions of enriched signal in experiment MCF-7 serum stim CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSerumstvdPkRep1 MCF-7 CTCF stv Pk CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEH003437 3437 GSM1006878 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMcf7CtcfSerumstvdPkRep1 serum_starved_media Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Regions of enriched signal in experiment MCF-7 serum starved CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfEstroPkRep1 MCF-7 est CTCF Pk CTCF MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001131 1131 GSM822309 Crawford UT-A p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipMcf7CtcfEstroPkRep1 estrogen Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) Regions of enriched signal in experiment MCF-7 estrogen CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfPk MCF-7 CTCF Pk CTCF MCF-7 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-12-28 2010-09-28 wgEncodeEH000598 598 GSM822305 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipMcf7CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment MCF-7 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycVehPkRep1 MCF-7 veh cMyc Pk c-Myc MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001133 1133 GSM822301 Crawford UT-A p-value cutoff: 0.05 hg19 exp wgEncodeOpenChromChipMcf7CmycVehPkRep1 vehicle Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) Regions of enriched signal in experiment MCF-7 vehicle cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycSerumstimPkRep1 MCF-7 cMyc stm Pk c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003436 3436 GSM1006877 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMcf7CmycSerumstimPkRep1 serum_stimulated_media Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Regions of enriched signal in experiment MCF-7 serum stim cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycSerumstvdPkRep1 MCF-7 cMyc stv Pk c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH003439 3439 GSM1006866 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipMcf7CmycSerumstvdPkRep1 serum_starved_media Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Regions of enriched signal in experiment MCF-7 serum starved cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycEstroPkRep1 MCF-7 est cMyc Pk c-Myc MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001134 1134 GSM822304 Crawford UT-A p-value cutoff: 0.05 hg19 1 exp wgEncodeOpenChromChipMcf7CmycEstroPkRep1 estrogen Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) Regions of enriched signal in experiment MCF-7 estrogen cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecPol2Pk HUVEC Pol2 Pk Pol2 HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-28 2010-06-28 wgEncodeEH000552 552 GSM822306 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipHuvecPol2Pk None Peaks RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HUVEC Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecCtcfPk HUVEC CTCF Pk CTCF HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-25 2010-06-25 wgEncodeEH000551 551 GSM822279 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipHuvecCtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HUVEC CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecCmycPk HUVEC cMyc Pk c-Myc HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-01 2010-07-01 wgEncodeEH000561 561 GSM822298 Crawford UT-A p-value cutoff: 0.01 hg18 exp wgEncodeOpenChromChipHuvecCmycPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HUVEC cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2Pol2Pk HepG2 Pol2 Pk Pol2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-09-29 2010-06-29 wgEncodeEH000554 554 GSM822284 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipHepg2Pol2Pk None Peaks RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HepG2 Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2CtcfPk HepG2 CTCF Pk CTCF HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000543 543 GSM822287 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipHepg2CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HepG2 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2CmycPk HepG2 cMyc Pk c-Myc HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-22 2009-12-22 wgEncodeEH000545 545 GSM822291 Crawford UT-A p-value cutoff: 0.01 hg18 exp wgEncodeOpenChromChipHepg2CmycPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HepG2 cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3Pol2Pk HeLa-S3 Pol2 Pk Pol2 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-28 2010-09-28 wgEncodeEH000597 597 GSM822273 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipHelas3Pol2Pk None Peaks RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HeLa-S3 Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3CtcfPk HeLa-S3 CTCF Pk CTCF HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000541 541 GSM822285 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipHelas3CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HeLa-S3 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3CmycPk HeLa-S3 cMyc Pk c-Myc HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000542 542 GSM822286 Crawford UT-A p-value cutoff: 0.01 hg18 exp wgEncodeOpenChromChipHelas3CmycPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment HeLa-S3 cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549Pol2PkRep1 A549 Pol2 Pk Pol2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002079 2079 GSM822288 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipA549Pol2PkRep1 None Peaks RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment A549 Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549CtcfPkRep1 A549 CTCF Pk CTCF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002078 2078 GSM822289 Crawford UT-A p-value cutoff: 0.05 1 exp wgEncodeOpenChromChipA549CtcfPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment A549 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562Pol2Pk K562 Pol2 Pk Pol2 K562 ChipSeq ENCODE June 2010 Freeze 2011-01-12 2009-09-29 2010-06-29 wgEncodeEH000555 555 GSM822275 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipK562Pol2Pk None Peaks RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment K562 Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562CtcfPk K562 CTCF Pk CTCF K562 ChipSeq ENCODE June 2010 Freeze 2011-01-12 2009-03-20 2009-12-20 wgEncodeEH000535 535 GSM822311 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipK562CtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment K562 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562CmycPk K562 cMyc Pk c-Myc K562 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-03-20 2009-12-20 wgEncodeEH000536 536 GSM822310 Crawford UT-A p-value cutoff: 0.01 hg18 exp wgEncodeOpenChromChipK562CmycPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment K562 cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescPol2Pk H1-hESC Pol2 Pk Pol2 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-10-02 2010-07-02 wgEncodeEH000563 563 GSM822300 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipH1hescPol2Pk None Peaks RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment H1-hESC Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescCtcfPk H1-hESC CTCF Pk CTCF H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-01 2010-07-01 wgEncodeEH000560 560 GSM822297 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipH1hescCtcfPk None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment H1-hESC CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescCmycPk H1-hESC cMyc Pk c-Myc H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-28 2010-09-27 wgEncodeEH000596 596 GSM822274 Crawford UT-A p-value cutoff: 0.01 hg18 exp wgEncodeOpenChromChipH1hescCmycPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment H1-hESC cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878Pol2Pk GM12878 Pol2 Pk Pol2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-12-23 2010-09-22 wgEncodeEH000592 592 GSM822270 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm12878Pol2Pk None Peaks RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12878 Pol2 TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878CtcfPkRep1 GM12878 CTCF Pk CTCF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000532 532 GSM822312 Crawford UT-A p-value cutoff: 0.05 hg18 exp wgEncodeOpenChromChipGm12878CtcfPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12878 CTCF TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878CmycPk GM12878 cMyc Pk c-Myc GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-02 2009-09-08 2010-06-08 wgEncodeEH000547 547 GSM822290 Crawford UT-A p-value cutoff: 0.001 hg18 exp wgEncodeOpenChromChipGm12878CmycPk None Peaks transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Regions of enriched signal in experiment GM12878 cMyc TFBS ChIP-seq Peaks from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipViewSignal ChIP F-Seq DS Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) Regulation 
wgEncodeOpenChromChipSpleenocInputSig Spleen Input DS Input Spleen_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003455 3455 GSM1006872 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipSpleenocInputSig Signal Primary frozen spleen tissue from NICHD donor IDs 1863 (Rep B1) and 4548 (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Spleen OC Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipSpleenocCtcfSigRep1 Spleen CTCF DS CTCF Spleen_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003464 3464 GSM1006883 Crawford UT-A fseq v 1.84, iff_Spleen 1 exp wgEncodeOpenChromChipSpleenocCtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen spleen tissue from NICHD donor IDs 1863 (Rep B1) and 4548 (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Spleen OC CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibInputSig ProgFib Input DS Input ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-12-23 2010-09-22 wgEncodeEH000593 593 GSM822269 Crawford UT-A privacy-noSequence fseq v 1.84 hg18 input wgEncodeOpenChromChipProgfibInputSig None Signal fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal ProgFib Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibPol2Sig ProgFib Pol2 DS Pol2 ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-10 2010-10-10 wgEncodeEH000606 606 GSM822282 Crawford UT-A privacy-noSequence fseq v 1.84, iff_FB0167P hg18 exp wgEncodeOpenChromChipProgfibPol2Sig None Signal RNA Polymerase II fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal ProgFib Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibCtcfSig ProgFib CTCF DS CTCF ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-02 2010-10-02 wgEncodeEH000600 600 GSM822272 Crawford UT-A privacy-noSequence fseq v 1.84, iff_FB0167P hg18 exp wgEncodeOpenChromChipProgfibCtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal ProgFib CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipPancreasocInputSig Pancreas Input DS Input Pancreas_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003454 3454 GSM1006871 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipPancreasocInputSig Signal Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Pancreas OC Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipPancreasocCtcfSigRep1 Pancreas CTCF DS CTCF Pancreas_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003463 3463 GSM1006881 Crawford UT-A fseq v 1.84, iff_Pancreas 1 exp wgEncodeOpenChromChipPancreasocCtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Pancreas OC CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipNhekCtcfSig NHEK CTCF DS CTCF NHEK ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-30 2010-06-30 wgEncodeEH000559 559 GSM822271 Crawford UT-A fseq v 1.84, iff_generic_female hg18 exp wgEncodeOpenChromChipNhekCtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal NHEK CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMedulloInputSig Medullo Input DS Input Medullo ChipSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003441 3441 GSM1006892 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipMedulloInputSig Signal medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Medullo Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMedulloCtcfSig Medullo CTCF DS CTCF Medullo ChipSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003440 3440 GSM1006893 Crawford UT-A fseq v 1.84, iff_D721 exp wgEncodeOpenChromChipMedulloCtcfSig Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Medullo CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLungocInputSig Lung Input DS Input Lung_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003453 3453 GSM1006880 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipLungocInputSig Signal Primary frozen lung tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase) and CF Center donor IDs DD006I (Rep B1 FAIRE) and DD007I (Rep B2 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Lung OC Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLungocCtcfSigRep1 Lung CTCF DS CTCF Lung_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003462 3462 GSM1006882 Crawford UT-A fseq v 1.84, iff_Lung 1 exp wgEncodeOpenChromChipLungocCtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen lung tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase) and CF Center donor IDs DD006I (Rep B1 FAIRE) and DD007I (Rep B2 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Lung OC CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapInputSig LNCaP Input DS Input LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003452 3452 GSM1006879 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipLncapInputSig Signal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal LNCaP Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapCtcfAndroSigRep1 LNCaP CTCF DS CTCF LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003460 3460 GSM1006887 Crawford UT-A fseq v 1.84, iff_LnCAP 1 exp wgEncodeOpenChromChipLncapCtcfAndroSigRep1 androgen Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) Signal LNCaP androgen CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapCtcfSigRep1 LNCaP CTCF DS CTCF LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003459 3459 GSM1006874 Crawford UT-A fseq v 1.84, iff_LnCAP 1 exp wgEncodeOpenChromChipLncapCtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal LNCaP CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipKidneyocInputSig Kidney Input DS Input Kidney_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003451 3451 GSM1006868 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipKidneyocInputSig Signal Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Kidney OC Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipKidneyocCtcfSigRep1 Kidney CTCF DS CTCF Kidney_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003461 3461 GSM1006886 Crawford UT-A fseq v 1.84, iff_Kidney 1 exp wgEncodeOpenChromChipKidneyocCtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Kidney OC CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHeartocInputSig Heart Input DS Input Heart_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003450 3450 GSM1006867 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipHeartocInputSig Signal Primary frozen heart tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B1 FAIRE), 4548 (Rep B2 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Heart OC Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm20000InputSig GM20000 Input DS Input GM20000 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003449 3449 GSM1006884 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipGm20000InputSig Signal lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM20000 Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm20000CtcfSigRep1 GM20000 CTCF DS CTCF GM20000 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003458 3458 GSM1006873 Crawford UT-A fseq v 1.84, iff_20000 1 exp wgEncodeOpenChromChipGm20000CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM20000 CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19240CtcfSig GM19240 CTCF DS CTCF GM19240 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-06 2010-07-06 wgEncodeEH000572 572 GSM822276 Crawford UT-A fseq v 1.84, iff_generic_female hg18 exp wgEncodeOpenChromChipGm19240CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM19240 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19239CtcfSig GM19239 CTCF DS CTCF GM19239 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000571 571 GSM822277 Crawford UT-A fseq v 1.84, iff_generic_male hg18 exp wgEncodeOpenChromChipGm19239CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM19239 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19238CtcfSig GM19238 CTCF DS CTCF GM19238 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000570 570 GSM822278 Crawford UT-A fseq v 1.84, iff_generic_female hg18 exp wgEncodeOpenChromChipGm19238CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM19238 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13977InputSig GM13977 Input DS Input GM13977 ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003444 3444 GSM1006889 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipGm13977InputSig Signal lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM13977 Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13977CtcfSigRep1 GM13977 CTCF DS CTCF GM13977 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003456 3456 GSM1006869 Crawford UT-A fseq v 1.84, iff_GM13977 1 exp wgEncodeOpenChromChipGm13977CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM13977 CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13976InputSig GM13976 Input DS Input GM13976 ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003443 3443 GSM1006894 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipGm13976InputSig Signal lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM13976 Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13976CtcfSigRep1 GM13976 CTCF DS CTCF GM13976 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003448 3448 GSM1006885 Crawford UT-A fseq v 1.84, iff_GM13976 1 exp wgEncodeOpenChromChipGm13976CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM13976 CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12892CtcfSig GM12892 CTCF DS CTCF GM12892 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-02 2010-07-02 wgEncodeEH000562 562 GSM822299 Crawford UT-A fseq v 1.84, iff_generic_female hg18 exp wgEncodeOpenChromChipGm12892CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM12892 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12891CtcfSig GM12891 CTCF DS CTCF GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000569 569 GSM822294 Crawford UT-A fseq v 1.84, iff_generic_male hg18 exp wgEncodeOpenChromChipGm12891CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM12891 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10266InputSig GM10266 Input DS Input GM10266 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003447 3447 GSM1006890 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipGm10266InputSig Signal lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM10266 Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10266CtcfSigRep1 GM10266 CTCF DS CTCF GM10266 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003457 3457 GSM1006870 Crawford UT-A fseq v 1.84, iff_GM10266 1 exp wgEncodeOpenChromChipGm10266CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM10266 CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10248InputSig GM10248 Input DS Input GM10248 ChipSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEH003442 3442 GSM1006895 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipGm10248InputSig Signal lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM10248 Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10248CtcfSigRep1 GM10248 CTCF DS CTCF GM10248 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003446 3446 GSM1006891 Crawford UT-A fseq v 1.84, iff_GM10248 1 exp wgEncodeOpenChromChipGm10248CtcfSigRep1 Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM10248 CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaInputSig Gliobla Input DS Input Gliobla ChipSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001129 1129 GSM822268 Crawford UT-A fseq v 1.84 hg19 input wgEncodeOpenChromChipGlioblaInputSig None Signal glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Gliobla Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaPol2Sig Gliobla Pol2 DS Pol2 Gliobla ChipSeq ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001136 1136 GSM822302 Crawford UT-A fseq v 1.84, iff_H54 hg19 exp wgEncodeOpenChromChipGlioblaPol2Sig None Signal RNA Polymerase II glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Gliobla Pol2 TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaCtcfSig Gliobla CTCF DS CTCF Gliobla ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-19 wgEncodeEH001135 1135 GSM822303 Crawford UT-A fseq v 1.84, iff_H54 hg19 exp wgEncodeOpenChromChipGlioblaCtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Gliobla CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipFibroblInputSig Fibrobl Input DS Input Fibrobl ChipSeq ENCODE Jan 2011 Freeze 2010-10-14 2011-07-14 wgEncodeEH001128 1128 GSM822267 Crawford UT-A privacy-noSequence fseq v 1.84 hg19 input wgEncodeOpenChromChipFibroblInputSig None Signal child fibroblast Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Fibrobl Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipFibroblCtcfSig Fibrobl CTCF DS CTCF Fibrobl ChipSeq ENCODE Jan 2011 Freeze 2010-10-13 2011-07-13 wgEncodeEH001127 1127 GSM822281 Crawford UT-A privacy-noSequence fseq v 1.84, iff_FB8470 hg19 exp wgEncodeOpenChromChipFibroblCtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. child fibroblast Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Fibrobl CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipColonocInputSig Colon Input DS Input Colon_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003445 3445 GSM1006888 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipColonocInputSig Signal Primary frozen colon tissue from NCTC donor IDs 10-0005A (Rep B1) and 10-0170A (Rep B2), African American and caucasian Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Colon OC Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMonocd14ro1746InputSig Mono-CD14+ Inp DS Input Monocytes-CD14+_RO01746 ChipSeq ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001137 1137 GSM822296 Crawford UT-A fseq v 1.84 hg19 input wgEncodeOpenChromChipMonocd14ro1746InputSig None Signal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal Monocytes-CD14+ Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7InputSig MCF-7 Input DS Input MCF-7 ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-12-22 2010-09-22 wgEncodeEH000589 589 GSM822283 Crawford UT-A fseq v 1.84 hg18 input wgEncodeOpenChromChipMcf7InputSig None Signal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal MCF-7 Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2SerumstimSig MCF-7 Pol2 stm DS Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003435 3435 GSM1006876 Crawford UT-A fseq v 1.84, iff_MCF7 exp wgEncodeOpenChromChipMcf7Pol2SerumstimSig serum_stimulated_media Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Signal MCF-7 serum stim Pol2 TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2SerumstvdSig MCF-7 Pol2 stv DS Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEH003438 3438 GSM1006865 Crawford UT-A fseq v 1.84, iff_MCF7 exp wgEncodeOpenChromChipMcf7Pol2SerumstvdSig serum_starved_media Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Signal MCF-7 serum starved Pol2 TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2Sig MCF-7 Pol2 DS Pol2 MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001130 1130 GSM822295 Crawford UT-A fseq v 1.84, iff_MCF7 hg19 exp wgEncodeOpenChromChipMcf7Pol2Sig None Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal MCF-7 Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfVehSig MCF-7 veh CTCF DS CTCF MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001132 1132 GSM822308 Crawford UT-A fseq v 1.84, iff_MCF7 hg19 exp wgEncodeOpenChromChipMcf7CtcfVehSig vehicle Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) Signal MCF-7 vehicle CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSerumstimSig MCF-7 CTCF stm DS CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003434 3434 GSM1006875 Crawford UT-A fseq v 1.84, iff_MCF7 exp wgEncodeOpenChromChipMcf7CtcfSerumstimSig serum_stimulated_media Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Signal MCF-7 serum stim CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSerumstvdSig MCF-7 CTCF stv DS CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEH003437 3437 GSM1006878 Crawford UT-A fseq v 1.84, iff_MCF7 exp wgEncodeOpenChromChipMcf7CtcfSerumstvdSig serum_starved_media Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Signal MCF-7 serum starved CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfEstroSig MCF-7 est CTCF DS CTCF MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001131 1131 GSM822309 Crawford UT-A fseq v 1.84, iff_MCF7 hg19 exp wgEncodeOpenChromChipMcf7CtcfEstroSig estrogen Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) Signal MCF-7 estrogen CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSig MCF-7 CTCF DS CTCF MCF-7 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-12-28 2010-09-28 wgEncodeEH000598 598 GSM822305 Crawford UT-A fseq v 1.84, iff_MCF7 hg18 exp wgEncodeOpenChromChipMcf7CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal MCF-7 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycVehSig MCF-7 veh cMyc DS c-Myc MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001133 1133 GSM822301 Crawford UT-A fseq v 1.84, iff_MCF7 hg19 exp wgEncodeOpenChromChipMcf7CmycVehSig vehicle Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) Signal MCF-7 vehicle cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycSerumstimSig MCF-7 cMyc stm DS c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003436 3436 GSM1006877 Crawford UT-A fseq v 1.84, iff_MCF7 exp wgEncodeOpenChromChipMcf7CmycSerumstimSig serum_stimulated_media Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. Signal MCF-7 serum stim cMyc TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycSerumstvdSig MCF-7 cMyc stv DS c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH003439 3439 GSM1006866 Crawford UT-A fseq v 1.84, iff_MCF7 exp wgEncodeOpenChromChipMcf7CmycSerumstvdSig serum_starved_media Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours Signal MCF-7 serum starved cMyc TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycEstroSig MCF-7 est cMyc DS c-Myc MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001134 1134 GSM822304 Crawford UT-A fseq v 1.84, iff_MCF7 hg19 exp wgEncodeOpenChromChipMcf7CmycEstroSig estrogen Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) Signal MCF-7 estrogen cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecInputSig HUVEC Input DS Input HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-18 2009-09-24 2010-06-24 wgEncodeEH000550 550 GSM822280 Crawford UT-A fseq v 1.84 hg18 input wgEncodeOpenChromChipHuvecInputSig None Signal umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HUVEC Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecPol2Sig HUVEC Pol2 DS Pol2 HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-28 2010-06-28 wgEncodeEH000552 552 GSM822306 Crawford UT-A fseq v 1.84, iff_HUVEC hg18 exp wgEncodeOpenChromChipHuvecPol2Sig None Signal RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HUVEC Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecCtcfSig HUVEC CTCF DS CTCF HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-25 2010-06-25 wgEncodeEH000551 551 GSM822279 Crawford UT-A fseq v 1.84, iff_HUVEC hg18 exp wgEncodeOpenChromChipHuvecCtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HUVEC CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecCmycSig HUVEC cMyc DS c-Myc HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-01 2010-07-01 wgEncodeEH000561 561 GSM822298 Crawford UT-A fseq v 1.84, iff_HUVEC hg18 exp wgEncodeOpenChromChipHuvecCmycSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HUVEC cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2InputSig HepG2 Input DS Input HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-18 2009-03-13 2009-12-13 wgEncodeEH000538 538 GSM822314 Crawford UT-A fseq v 1.84 hg18 input wgEncodeOpenChromChipHepg2InputSig None Signal hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HepG2 Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2Pol2Sig HepG2 Pol2 DS Pol2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-09-29 2010-06-29 wgEncodeEH000554 554 GSM822284 Crawford UT-A fseq v 1.84, iff_HepG2 hg18 exp wgEncodeOpenChromChipHepg2Pol2Sig None Signal RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HepG2 Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2CtcfSig HepG2 CTCF DS CTCF HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000543 543 GSM822287 Crawford UT-A fseq v 1.84, iff_HepG2 hg18 exp wgEncodeOpenChromChipHepg2CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HepG2 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2CmycSig HepG2 cMyc DS c-Myc HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-22 2009-12-22 wgEncodeEH000545 545 GSM822291 Crawford UT-A fseq v 1.84, iff_HepG2 hg18 exp wgEncodeOpenChromChipHepg2CmycSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HepG2 cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3InputSig HeLa-S3 Input DS Input HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-18 2009-03-16 2009-12-16 wgEncodeEH000539 539 GSM822313 Crawford UT-A fseq v 1.84 hg18 input wgEncodeOpenChromChipHelas3InputSig None Signal cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HeLa-S3 Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3Pol2Sig HeLa-S3 Pol2 DS Pol2 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-28 2010-09-28 wgEncodeEH000597 597 GSM822273 Crawford UT-A fseq v 1.84, iff_HelaS3 hg18 exp wgEncodeOpenChromChipHelas3Pol2Sig None Signal RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HeLa-S3 Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3CtcfSig HeLa-S3 CTCF DS CTCF HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000541 541 GSM822285 Crawford UT-A fseq v 1.84, iff_HelaS3 hg18 exp wgEncodeOpenChromChipHelas3CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HeLa-S3 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3CmycSig HeLa-S3 cMyc DS c-Myc HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000542 542 GSM822286 Crawford UT-A fseq v 1.84, iff_HelaS3 hg18 exp wgEncodeOpenChromChipHelas3CmycSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal HeLa-S3 cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549InputSig A549 Input DS Input A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-27 2012-06-27 wgEncodeEH002077 2077 GSM822307 Crawford UT-A fseq v 1.84 input wgEncodeOpenChromChipA549InputSig None Signal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal A549 Input TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549Pol2Sig A549 Pol2 DS Pol2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002079 2079 GSM822288 Crawford UT-A fseq v 1.84, iff_A549 exp wgEncodeOpenChromChipA549Pol2Sig None Signal RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal A549 Pol2 TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549CtcfSig A549 CTCF DS CTCF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002078 2078 GSM822289 Crawford UT-A fseq v 1.84, iff_A549 exp wgEncodeOpenChromChipA549CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal A549 CTCF TFBS ChIP-seq Density Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562InputSig K562 Input DS Input K562 ChipSeq ENCODE June 2010 Freeze 2010-06-18 2008-12-05 2009-08-05 wgEncodeEH000529 529 GSM822293 Crawford UT-A fseq v 1.84 hg18 input wgEncodeOpenChromChipK562InputSig None Signal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal K562 Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562Pol2Sig K562 Pol2 DS Pol2 K562 ChipSeq ENCODE June 2010 Freeze 2011-01-12 2009-09-29 2010-06-29 wgEncodeEH000555 555 GSM822275 Crawford UT-A fseq v 1.84, iff_K562 hg18 exp wgEncodeOpenChromChipK562Pol2Sig None Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal K562 Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562CtcfSig K562 CTCF DS CTCF K562 ChipSeq ENCODE June 2010 Freeze 2011-01-12 2009-02-27 2009-11-27 wgEncodeEH000535 535 GSM822311 Crawford UT-A fseq v 1.84, iff_K562 hg18 exp wgEncodeOpenChromChipK562CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal K562 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562CmycSig K562 cMyc DS c-Myc K562 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-02-27 2009-11-27 wgEncodeEH000536 536 GSM822310 Crawford UT-A fseq v 1.84, iff_K562 hg18 exp wgEncodeOpenChromChipK562CmycSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal K562 cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescPol2Sig H1-hESC Pol2 DS Pol2 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-10-02 2010-07-02 wgEncodeEH000563 563 GSM822300 Crawford UT-A fseq v 1.84, iff_generic_male hg18 exp wgEncodeOpenChromChipH1hescPol2Sig None Signal RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal H1-hESC Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescCtcfSig H1-hESC CTCF DS CTCF H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-01 2010-07-01 wgEncodeEH000560 560 GSM822297 Crawford UT-A fseq v 1.84, iff_generic_male hg18 exp wgEncodeOpenChromChipH1hescCtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal H1-hESC CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescCmycSig H1-hESC cMyc DS c-Myc H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-28 2010-09-27 wgEncodeEH000596 596 GSM822274 Crawford UT-A fseq v 1.84, iff_generic_male hg18 exp wgEncodeOpenChromChipH1hescCmycSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal H1-hESC cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878InputSig GM12878 Input DS Input GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2008-11-07 2009-07-07 wgEncodeEH000528 528 GSM822292 Crawford UT-A fseq v 1.84 hg18 input wgEncodeOpenChromChipGm12878InputSig None Signal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM12878 Input TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878Pol2Sig GM12878 Pol2 DS Pol2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-12-23 2010-09-22 wgEncodeEH000592 592 GSM822270 Crawford UT-A fseq v 1.84, iff_GM12878 hg18 exp wgEncodeOpenChromChipGm12878Pol2Sig None Signal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM12878 Pol2 TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878CtcfSig GM12878 CTCF DS CTCF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000532 532 GSM822312 Crawford UT-A fseq v 1.84, iff_GM12878 hg18 exp wgEncodeOpenChromChipGm12878CtcfSig None Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM12878 CTCF TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878CmycSig GM12878 cMyc DS c-Myc GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-02 2009-09-08 2010-06-08 wgEncodeEH000547 547 GSM822290 Crawford UT-A fseq v 1.84, iff_GM12878 hg18 exp wgEncodeOpenChromChipGm12878CmycSig None Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Signal GM12878 cMyc TFBS ChIP-seq Density Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipViewSigBo Base OS Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin) Regulation 
wgEncodeOpenChromChipSpleenocCtcfBaseOverlapSignalRep1 Spleen CTCF OS CTCF Spleen_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003464 3464 GSM1006883 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipSpleenocCtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen spleen tissue from NICHD donor IDs 1863 (Rep B1) and 4548 (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Spleen OC CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibPol2BaseOverlapSignal ProgFib Pol2 OS Pol2 ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-10 2010-10-10 wgEncodeEH000606 606 GSM822282 Crawford UT-A privacy-noSequence baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipProgfibPol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. ProgFib Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipProgfibCtcfBaseOverlapSignal ProgFib CTCF OS CTCF ProgFib ChipSeq ENCODE June 2010 Freeze 2010-06-19 2010-01-02 2010-10-02 wgEncodeEH000600 600 GSM822272 Crawford UT-A privacy-noSequence baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipProgfibCtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. ProgFib CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipPancreasocCtcfBaseOverlapSignalRep1 Pancreas CTCF OS CTCF Pancreas_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003463 3463 GSM1006881 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipPancreasocCtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen pancreas tissue from NCTC donor IDs 09-0144A (Rep B1) and 10-0021A (Rep B2) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Pancreas OC CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipNhekCtcfBaseOverlapSignal NHEK CTCF OS CTCF NHEK ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-30 2010-06-30 wgEncodeEH000559 559 GSM822271 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipNhekCtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. NHEK CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMedulloCtcfBaseOverlapSignal Medullo CTCF OS CTCF Medullo ChipSeq ENCODE Jul 2012 Freeze 2012-07-06 2013-04-06 wgEncodeEH003440 3440 GSM1006893 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMedulloCtcfBaseOverlapSignal Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. medulloblastoma (aka D721), surgical resection from a patient with medulloblastoma as described by Darrell Bigner (1997) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Medullo CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLungocCtcfBaseOverlapSignalRep1 Lung CTCF OS CTCF Lung_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003462 3462 GSM1006882 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipLungocCtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen lung tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase) and CF Center donor IDs DD006I (Rep B1 FAIRE) and DD007I (Rep B2 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Lung OC CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapCtcfAndroBaseOverlapSignalRep1 LNCaP CTCF OS CTCF LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003460 3460 GSM1006887 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipLncapCtcfAndroBaseOverlapSignalRep1 androgen Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 12 hrs with 1 nM Methyltrienolone (R1881) (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. LNCaP androgen CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipLncapCtcfBaseOverlapSignalRep1 LNCaP CTCF OS CTCF LNCaP ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003459 3459 GSM1006874 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipLncapCtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. LNCaP CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipKidneyocCtcfBaseOverlapSignalRep1 Kidney CTCF OS CTCF Kidney_OC ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-04-30 wgEncodeEH003461 3461 GSM1006886 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipKidneyocCtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Primary frozen kidney tissue from NICHD donor IDs 1104 (Rep B1 DNase), 602 (Rep B2 DNase), 1442 (Rep B3 DNase), 1863 (Rep B3 FAIRE) and NCTC donor ID 10-0022A (Rep B1 FAIRE) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Kidney OC CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm20000CtcfBaseOverlapSignalRep1 GM20000 CTCF OS CTCF GM20000 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-30 wgEncodeEH003458 3458 GSM1006873 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipGm20000CtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM20000 CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19240CtcfBaseOverlapSignal GM19240 CTCF OS CTCF GM19240 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-06 2010-07-06 wgEncodeEH000572 572 GSM822276 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm19240CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM19240 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19239CtcfBaseOverlapSignal GM19239 CTCF OS CTCF GM19239 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000571 571 GSM822277 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm19239CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM19239 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm19238CtcfBaseOverlapSignal GM19238 CTCF OS CTCF GM19238 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000570 570 GSM822278 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm19238CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM19238 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13977CtcfBaseOverlapSignalRep1 GM13977 CTCF OS CTCF GM13977 ChipSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003456 3456 GSM1006869 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipGm13977CtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, Clinically affected; microcephaly; low frontal hairline; synophris; "penciled" arched eyebrows; short nose; crescent shaped mouth; hirsutism; micromelia; short thumbs; mental retardation; clinically normal monozygotic twin sister is GM13976 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM13977 CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm13976CtcfBaseOverlapSignalRep1 GM13976 CTCF OS CTCF GM13976 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003448 3448 GSM1006885 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipGm13976CtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, clinically normal; monozygotic twin sister with Cornelia De Lange syndrome is GM13977 Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM13976 CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12892CtcfBaseOverlapSignal GM12892 CTCF OS CTCF GM12892 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-02 2010-07-02 wgEncodeEH000562 562 GSM822299 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm12892CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12892 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12891CtcfBaseOverlapSignal GM12891 CTCF OS CTCF GM12891 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-06 2010-07-06 wgEncodeEH000569 569 GSM822294 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm12891CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12891 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10266CtcfBaseOverlapSignalRep1 GM10266 CTCF OS CTCF GM10266 ChipSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEH003457 3457 GSM1006870 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipGm10266CtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, De Lange phenotype; developmental delay; profound retardation; seizures; 3 cousins are also affected; 46,XY,-22,+der (22)t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM10266 CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm10248CtcfBaseOverlapSignalRep1 GM10248 CTCF OS CTCF GM10248 ChipSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEH003446 3446 GSM1006891 Crawford UT-A baseAlignCounts.pl v 1 1 exp wgEncodeOpenChromChipGm10248CtcfBaseOverlapSignalRep1 Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lymphoblastoid cell line, Clinically normal; 4 paternal cousins have Cornelia de Lange syndrome; 46,XY, t(3;22)(q25.3;p12) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM10248 CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaPol2BaseOverlapSignal Gliobla Pol2 OS Pol2 Gliobla ChipSeq ENCODE Jan 2011 Freeze 2011-01-17 2011-10-17 wgEncodeEH001136 1136 GSM822302 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipGlioblaPol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Gliobla Pol2 TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGlioblaCtcfBaseOverlapSignal Gliobla CTCF OS CTCF Gliobla ChipSeq ENCODE Jan 2011 Freeze 2010-10-20 2011-07-19 wgEncodeEH001135 1135 GSM822303 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipGlioblaCtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. glioblastoma, these cells (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line (Bao et al., 2006) that has been thoroughly described by S Bigner (1981). (PMID: 7252524) Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Gliobla CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal Fibrobl CTCF OS CTCF Fibrobl ChipSeq ENCODE Jan 2011 Freeze 2010-10-13 2011-07-13 wgEncodeEH001127 1127 GSM822281 Crawford UT-A privacy-noSequence baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. child fibroblast Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. Fibrobl CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2SerumstimBaseOverlapSignal MCF-7 Pol2 stm OS Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003435 3435 GSM1006876 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMcf7Pol2SerumstimBaseOverlapSignal serum_stimulated_media Base_Overlap_Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 serum stim Pol2 TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2SerumstvdBaseOverlapSignal MCF-7 Pol2 stv OS Pol2 MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEH003438 3438 GSM1006865 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMcf7Pol2SerumstvdBaseOverlapSignal serum_starved_media Base_Overlap_Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 serum starved Pol2 TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7Pol2BaseOverlapSignal MCF-7 Pol2 OS Pol2 MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-15 2011-07-15 wgEncodeEH001130 1130 GSM822295 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipMcf7Pol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfVehBaseOverlapSignal MCF-7 veh CTCF OS CTCF MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001132 1132 GSM822308 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipMcf7CtcfVehBaseOverlapSignal vehicle Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 vehicle CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSerumstimBaseOverlapSignal MCF-7 CTCF stm OS CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003434 3434 GSM1006875 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMcf7CtcfSerumstimBaseOverlapSignal serum_stimulated_media Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 serum stim CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfSerumstvdBaseOverlapSignal MCF-7 CTCF stv OS CTCF MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEH003437 3437 GSM1006878 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMcf7CtcfSerumstvdBaseOverlapSignal serum_starved_media Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 serum starved CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfEstroBaseOverlapSignal MCF-7 est CTCF OS CTCF MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001131 1131 GSM822309 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipMcf7CtcfEstroBaseOverlapSignal estrogen Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 estrogen CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CtcfBaseOverlapSignal MCF-7 CTCF OS CTCF MCF-7 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-12-28 2010-09-28 wgEncodeEH000598 598 GSM822305 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipMcf7CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycVehBaseOverlapSignal MCF-7 veh cMyc OS c-Myc MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001133 1133 GSM822301 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipMcf7CmycVehBaseOverlapSignal vehicle Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Charcoal stripped hormone-free FBS for 72 hours (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 vehicle cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycSerumstimBaseOverlapSignal MCF-7 cMyc stm OS c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-02-11 2012-11-11 wgEncodeEH003436 3436 GSM1006877 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMcf7CmycSerumstimBaseOverlapSignal serum_stimulated_media Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media that contains no FBS for 36 hours, then switched back to normal serum levels (10% FBS) for 3 hours. An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 serum stim cMyc TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycSerumstvdBaseOverlapSignal MCF-7 cMyc stv OS c-Myc MCF-7 ChipSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEH003439 3439 GSM1006866 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipMcf7CmycSerumstvdBaseOverlapSignal serum_starved_media Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 serum starved cMyc TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipMcf7CmycEstroBaseOverlapSignal MCF-7 est cMyc OS c-Myc MCF-7 ChipSeq ENCODE Jan 2011 Freeze 2010-10-16 2011-07-16 wgEncodeEH001134 1134 GSM822304 Crawford UT-A baseAlignCounts.pl v 1 hg19 exp wgEncodeOpenChromChipMcf7CmycEstroBaseOverlapSignal estrogen Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin 45 min with 100 nM Estradiol (Crawford) An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. MCF-7 estrogen cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecPol2BaseOverlapSignal HUVEC Pol2 OS Pol2 HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-28 2010-06-28 wgEncodeEH000552 552 GSM822306 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHuvecPol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HUVEC Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecCtcfBaseOverlapSignal HUVEC CTCF OS CTCF HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-25 2010-06-25 wgEncodeEH000551 551 GSM822279 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHuvecCtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HUVEC CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHuvecCmycBaseOverlapSignal HUVEC cMyc OS c-Myc HUVEC ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-10-01 2010-07-01 wgEncodeEH000561 561 GSM822298 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHuvecCmycBaseOverlapSignal None Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease umbilical vein endothelial cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HUVEC cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2Pol2BaseOverlapSignal HepG2 Pol2 OS Pol2 HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-09-29 2010-06-29 wgEncodeEH000554 554 GSM822284 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHepg2Pol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HepG2 Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2CtcfBaseOverlapSignal HepG2 CTCF OS CTCF HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000543 543 GSM822287 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHepg2CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HepG2 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHepg2CmycBaseOverlapSignal HepG2 cMyc OS c-Myc HepG2 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-22 2009-12-22 wgEncodeEH000545 545 GSM822291 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHepg2CmycBaseOverlapSignal None Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease hepatocellular carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HepG2 cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3Pol2BaseOverlapSignal HeLa-S3 Pol2 OS Pol2 HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-28 2010-09-28 wgEncodeEH000597 597 GSM822273 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHelas3Pol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HeLa-S3 Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3CtcfBaseOverlapSignal HeLa-S3 CTCF OS CTCF HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000541 541 GSM822285 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHelas3CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HeLa-S3 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipHelas3CmycBaseOverlapSignal HeLa-S3 cMyc OS c-Myc HeLa-S3 ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-03-21 2009-12-21 wgEncodeEH000542 542 GSM822286 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipHelas3CmycBaseOverlapSignal None Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease cervical carcinoma Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. HeLa-S3 cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549Pol2BaseOverlapSignal A549 Pol2 OS Pol2 A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002079 2079 GSM822288 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipA549Pol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. A549 Pol2 TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipA549CtcfBaseOverlapSignal A549 CTCF OS CTCF A549 ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-29 wgEncodeEH002078 2078 GSM822289 Crawford UT-A baseAlignCounts.pl v 1 exp wgEncodeOpenChromChipA549CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. A549 CTCF TFBS ChIP-seq Overlap Signal from ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562Pol2BaseOverlapSignal K562 Pol2 OS Pol2 K562 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-09-29 2010-06-29 wgEncodeEH000555 555 GSM822275 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipK562Pol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562CtcfBaseOverlapSignal K562 CTCF OS CTCF K562 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-02-27 2009-11-27 wgEncodeEH000535 535 GSM822311 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipK562CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipK562CmycBaseOverlapSignal K562 cMyc OS c-Myc K562 ChipSeq ENCODE June 2010 Freeze 2010-06-17 2009-02-27 2009-11-27 wgEncodeEH000536 536 GSM822310 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipK562CmycBaseOverlapSignal None Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. K562 cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescPol2BaseOverlapSignal H1-hESC Pol2 OS Pol2 H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-22 2009-10-02 2010-07-02 wgEncodeEH000563 563 GSM822300 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipH1hescPol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. H1-hESC Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescCtcfBaseOverlapSignal H1-hESC CTCF OS CTCF H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-10-01 2010-07-01 wgEncodeEH000560 560 GSM822297 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipH1hescCtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. H1-hESC CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipH1hescCmycBaseOverlapSignal H1-hESC cMyc OS c-Myc H1-hESC ChipSeq ENCODE June 2010 Freeze 2010-06-16 2009-12-28 2010-09-27 wgEncodeEH000596 596 GSM822274 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipH1hescCmycBaseOverlapSignal None Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease embryonic stem cells Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. H1-hESC cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878Pol2BaseOverlapSignal GM12878 Pol2 OS Pol2 GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-12-23 2010-09-22 wgEncodeEH000592 592 GSM822270 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm12878Pol2BaseOverlapSignal None Base_Overlap_Signal RNA Polymerase II B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12878 Pol2 TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878CtcfBaseOverlapSignal GM12878 CTCF OS CTCF GM12878 ChipSeq ENCODE Jan 2011 Freeze 2010-10-01 2011-07-01 wgEncodeEH000532 532 GSM822312 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm12878CtcfBaseOverlapSignal None Base_Overlap_Signal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12878 CTCF TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeOpenChromChipGm12878CmycBaseOverlapSignal GM12878 cMyc OS c-Myc GM12878 ChipSeq ENCODE June 2010 Freeze 2010-06-02 2009-09-08 2010-06-08 wgEncodeEH000547 547 GSM822290 Crawford UT-A baseAlignCounts.pl v 1 hg18 exp wgEncodeOpenChromChipGm12878CmycBaseOverlapSignal None Base_Overlap_Signal transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Chromatin IP Sequencing Crawford Iyer - University of Texas at Austin An alternative version of the F-Seq Density Signal track annotation that provides a higher resolution view of the raw sequence data. This track also includes the combined set of sequences from all replicates. For each sequence, the aligned read is extended 5 bp in both directions from its 5' aligned end where DNase cut the DNA. The score at each base pair represents the number of extended fragments that overlap the base pair. GM12878 cMyc TFBS ChIP-seq Overlap Signal ENCODE/OpenChrom-UTA Regulation 
wgEncodeUwAffyExonArray UW Affy Exon GSE19090 Affymetrix Exon Array from ENCODE/University of Washington Expression Description This track displays human tissue microarray data using Affymetrix Human Exon 1.0 GeneChip and was produced as part of the ENCODE Project. This track in the hg19 assembly is a continuation of the work displayed in the hg18 assembly with additional cell lines. Display Conventions and Configuration The display for this track shows probe location and signal value as grayscale-colored items where higher signal values correspond to darker-colored blocks. Items with score of 1000 are in the highest 10% quantile for signal value of that particular cell type. Similarly, items scoring 900 are the next 10% quantile and at the bottom of scale, items scoring 100 are in the lowest 10% quantile for signal value. The subtracks within this composite annotation track correspond to data from different cell types and tissues. The configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For information regarding specific microarray probes, look under the &quot;Expression&quot; track group and turn on the Affy Exon Array track. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. A subset of the cells were stored frozen in RNAlater. For the WI-38 Tamoxifen-treated (4OHTAM_20nM_72hr) cell type, cells at 50-80% confluency were treated for 72 hours with 20 nM 4-hydroxytamoxifen in growth medium (from a 1000X working stock in absolute ethanol). At harvest, greater than 95% of DNA synthesis was inhibited and the cells had an induced fusiform/round morphology with greater than 95% showing dramatic senescence-associated heterochromatic foci. Total RNA was labeled and hybridized to Affymetrix Human Exon 1.0 ST V2 arrays using hg19 probesets. Exon and gene level expression analysis were carried out using Affymetrix ExACT 1.2.1 and Affymetrix Expression Console 1.1 software tools. Samples were quantile normalized for background correction and Probe Logarithmic Intensity Error summarized. More detailed methods are here. Release Notes This is release 4 (Jul 2012) of this track. A patch update has removed previously released K562 zinc-finger experiments due to a data merging issue. This update adds in H7-hESC cells that have been differentiated with different time courses. Verification Data were verified by sequencing biological replicates displaying correlation coefficient of 0.9 or greater. Credits These data were generated by the University of Washington ENCODE group. Contact: Richard Sandstrom References Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUwAffyExonArrayWi38OhtamSimpleSignalRep2 WI-38 tam 2 WI-38 AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000830 830 GSM651583 Stam UW 2 wgEncodeUwAffyExonArrayWi38OhtamSimpleSignalRep2 4OHTAM_20nM_72hr SimpleSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Simple Signal WI-38 (tamoxifen) Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayWi38SimpleSignalRep2 WI-38 2 WI-38 AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000829 829 GSM651581 Stam UW 2 wgEncodeUwAffyExonArrayWi38SimpleSignalRep2 SimpleSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal WI-38 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayWi38OhtamSimpleSignalRep1 WI-38 tam 1 WI-38 AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000830 830 GSM651582 Stam UW 1 wgEncodeUwAffyExonArrayWi38OhtamSimpleSignalRep1 4OHTAM_20nM_72hr SimpleSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Simple Signal WI-38 (tamoxifen) Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayWi38SimpleSignalRep1 WI-38 1 WI-38 AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000829 829 GSM651580 Stam UW 1 wgEncodeUwAffyExonArrayWi38SimpleSignalRep1 SimpleSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal WI-38 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayWerirb1SimpleSignalRep1 WERI-Rb-1 1 WERI-Rb-1 AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002163 2163 GSM824870 Stam UW RS17575 1 wgEncodeUwAffyExonArrayWerirb1SimpleSignalRep1 SimpleSignal retinoblastoma (PMID: 844036) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal WERI-Rb-1 Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayTh1SimpleSignalRep1 Th1 1 Th1 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000364 364 GSM472914 Stam UW hg18 1 wgEncodeUwAffyExonArrayTh1SimpleSignalRep1 SimpleSignal primary Th1 T cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal Th1 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySknshraSimpleSignalRep2 SK-N-SH_RA 2 SK-N-SH_RA AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-06-29 2010-03-29 wgEncodeEH000358 358 GSM472912 Stam UW hg18 2 wgEncodeUwAffyExonArraySknshraSimpleSignalRep2 SimpleSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SK-N-SH_RA Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySknshraSimpleSignalRep1 SK-N-SH_RA 1 SK-N-SH_RA AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000358 358 GSM472913 Stam UW hg18 1 wgEncodeUwAffyExonArraySknshraSimpleSignalRep1 SimpleSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SK-N-SH_RA Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySknmcSimpleSignalRep2 SK-N-MC 2 SK-N-MC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002162 2162 GSM824869 Stam UW RS17574 2 wgEncodeUwAffyExonArraySknmcSimpleSignalRep2 SimpleSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SK-N-MC Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySknmcSimpleSignalRep1 SK-N-MC 1 SK-N-MC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002162 2162 GSM824868 Stam UW RS17573 1 wgEncodeUwAffyExonArraySknmcSimpleSignalRep1 SimpleSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SK-N-MC Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySkmcSimpleSignalRep2 SKMC 2 SKMC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000363 363 GSM472911 Stam UW hg18 2 wgEncodeUwAffyExonArraySkmcSimpleSignalRep2 SimpleSignal skeletal muscle cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SKMC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySkmcSimpleSignalRep1 SKMC 1 SKMC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000363 363 GSM510509 Stam UW hg18 1 wgEncodeUwAffyExonArraySkmcSimpleSignalRep1 SimpleSignal skeletal muscle cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SKMC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySaecSimpleSignalRep2 SAEC 2 SAEC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000374 374 GSM472922 Stam UW hg18 2 wgEncodeUwAffyExonArraySaecSimpleSignalRep2 SimpleSignal small airway epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SAEC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArraySaecSimpleSignalRep1 SAEC 1 SAEC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000374 374 GSM472923 Stam UW hg18 1 wgEncodeUwAffyExonArraySaecSimpleSignalRep1 SimpleSignal small airway epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal SAEC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayRptecSimpleSignalRep2 RPTEC 2 RPTEC AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000828 828 GSM651566 Stam UW 2 wgEncodeUwAffyExonArrayRptecSimpleSignalRep2 SimpleSignal renal proximal tubule epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal RPTEC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayRptecSimpleSignalRep1 RPTEC 1 RPTEC AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000828 828 GSM651565 Stam UW 1 wgEncodeUwAffyExonArrayRptecSimpleSignalRep1 SimpleSignal renal proximal tubule epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal RPTEC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayPrecSimpleSignalRep2 PrEC 2 PrEC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002161 2161 GSM824858 Stam UW RS19008 2 wgEncodeUwAffyExonArrayPrecSimpleSignalRep2 SimpleSignal prostate epithelial cell line Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal PrEC Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayPrecSimpleSignalRep1 PrEC 1 PrEC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002161 2161 GSM824857 Stam UW RS19007 1 wgEncodeUwAffyExonArrayPrecSimpleSignalRep1 SimpleSignal prostate epithelial cell line Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal PrEC Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayPanc1SimpleSignalRep2 PANC-1 2 PANC-1 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000373 373 GSM472938 Stam UW hg18 2 wgEncodeUwAffyExonArrayPanc1SimpleSignalRep2 SimpleSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal PANC-1 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayPanc1SimpleSignalRep1 PANC-1 1 PANC-1 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000373 373 GSM472939 Stam UW hg18 1 wgEncodeUwAffyExonArrayPanc1SimpleSignalRep1 SimpleSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal PANC-1 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNt2d1SimpleSignalRep2 NT2-D1 2 NT2-D1 AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002160 2160 GSM824856 Stam UW RS19006 2 wgEncodeUwAffyExonArrayNt2d1SimpleSignalRep2 SimpleSignal malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NT2-D1 Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNt2d1SimpleSignalRep1 NT2-D1 1 NT2-D1 AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002160 2160 GSM824855 Stam UW RS19005 1 wgEncodeUwAffyExonArrayNt2d1SimpleSignalRep1 SimpleSignal malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID: 6694356) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NT2-D1 Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhlfSimpleSignalRep2 NHLF 2 NHLF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000391 391 GSM510579 Stam UW hg18 2 wgEncodeUwAffyExonArrayNhlfSimpleSignalRep2 SimpleSignal lung fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHLF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhlfSimpleSignalRep1 NHLF 1 NHLF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000391 391 GSM510577 Stam UW hg18 1 wgEncodeUwAffyExonArrayNhlfSimpleSignalRep1 SimpleSignal lung fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHLF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhekSimpleSignalRep1 NHEK 1 NHEK AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000372 372 GSM472937 Stam UW hg18 1 wgEncodeUwAffyExonArrayNhekSimpleSignalRep1 SimpleSignal epidermal keratinocytes Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHEK Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhdfneoSimpleSignalRep2 NHDF-neo 2 NHDF-neo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000390 390 GSM510557 Stam UW hg18 2 wgEncodeUwAffyExonArrayNhdfneoSimpleSignalRep2 SimpleSignal neonatal dermal fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHDF-neo Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhdfneoSimpleSignalRep1 NHDF-neo 1 NHDF-neo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000390 390 GSM510554 Stam UW hg18 1 wgEncodeUwAffyExonArrayNhdfneoSimpleSignalRep1 SimpleSignal neonatal dermal fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHDF-neo Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhdfadSimpleSignalRep2 NHDF-Ad 2 NHDF-Ad AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000822 822 GSM580018 Stam UW 2 wgEncodeUwAffyExonArrayNhdfadSimpleSignalRep2 SimpleSignal adult dermal fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHDF-Ad Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhdfadSimpleSignalRep1 NHDF-Ad 1 NHDF-Ad AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000822 822 GSM580017 Stam UW 1 wgEncodeUwAffyExonArrayNhdfadSimpleSignalRep1 SimpleSignal adult dermal fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHDF-Ad Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhbeSimpleSignalRep2 NHBE 2 NHBE AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002159 2159 GSM824854 Stam UW RS19004 2 wgEncodeUwAffyExonArrayNhbeSimpleSignalRep2 SimpleSignal bronchial epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHBE Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhbeSimpleSignalRep1 NHBE 1 NHBE AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002159 2159 GSM824853 Stam UW RS19003 1 wgEncodeUwAffyExonArrayNhbeSimpleSignalRep1 SimpleSignal bronchial epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NHBE Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhaSimpleSignalRep2 NH-A 2 NH-A AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000821 821 GSM580044 Stam UW 2 wgEncodeUwAffyExonArrayNhaSimpleSignalRep2 SimpleSignal astrocytes (also called Astrocy) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NH-A Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNhaSimpleSignalRep1 NH-A 1 NH-A AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000821 821 GSM580043 Stam UW 1 wgEncodeUwAffyExonArrayNhaSimpleSignalRep1 SimpleSignal astrocytes (also called Astrocy) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NH-A Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNb4SimpleSignalRep2 NB4 2 NB4 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000371 371 GSM510513 Stam UW hg18 2 wgEncodeUwAffyExonArrayNb4SimpleSignalRep2 SimpleSignal acute promyelocytic leukemia cell line. (PMID: 1995093) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NB4 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayNb4SimpleSignalRep1 NB4 1 NB4 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000371 371 GSM510512 Stam UW hg18 1 wgEncodeUwAffyExonArrayNb4SimpleSignalRep1 SimpleSignal acute promyelocytic leukemia cell line. (PMID: 1995093) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal NB4 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayLncapSimpleSignalRep2 LNCaP 2 LNCaP AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000827 827 GSM651579 Stam UW 2 wgEncodeUwAffyExonArrayLncapSimpleSignalRep2 SimpleSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal LNCaP Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayLncapSimpleSignalRep1 LNCaP 1 LNCaP AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000827 827 GSM651578 Stam UW 1 wgEncodeUwAffyExonArrayLncapSimpleSignalRep1 SimpleSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal LNCaP Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayJurkatSimpleSignalRep2 Jurkat 2 Jurkat AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000369 369 GSM510511 Stam UW hg18 2 wgEncodeUwAffyExonArrayJurkatSimpleSignalRep2 SimpleSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal Jurkat Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayJurkatSimpleSignalRep1 Jurkat 1 Jurkat AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000369 369 GSM472928 Stam UW hg18 1 wgEncodeUwAffyExonArrayJurkatSimpleSignalRep1 SimpleSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal Jurkat Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHvmfSimpleSignalRep2 HVMF 2 HVMF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000820 820 GSM580038 Stam UW 2 wgEncodeUwAffyExonArrayHvmfSimpleSignalRep2 SimpleSignal villous mesenchymal fibroblast cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HVMF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHvmfSimpleSignalRep1 HVMF 1 HVMF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000820 820 GSM580037 Stam UW 1 wgEncodeUwAffyExonArrayHvmfSimpleSignalRep1 SimpleSignal villous mesenchymal fibroblast cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HVMF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHsmmtSimpleSignalRep2 HSMMtube 2 HSMMtube AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH000826 826 GSM824861 Stam UW RS17572 2 wgEncodeUwAffyExonArrayHsmmtSimpleSignalRep2 SimpleSignal skeletal muscle myotubes differentiated from the HSMM cell line Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HSMMtube Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHsmmtSimpleSignalRep1 HSMMtube 1 HSMMtube AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000826 826 GSM651576 Stam UW 1 wgEncodeUwAffyExonArrayHsmmtSimpleSignalRep1 SimpleSignal skeletal muscle myotubes differentiated from the HSMM cell line Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HSMMtube Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHsmmSimpleSignalRep2 HSMM 2 HSMM AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000833 833 GSM651575 Stam UW 2 wgEncodeUwAffyExonArrayHsmmSimpleSignalRep2 SimpleSignal skeletal muscle myoblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HSMM Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHsmmSimpleSignalRep1 HSMM 1 HSMM AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000833 833 GSM651574 Stam UW 1 wgEncodeUwAffyExonArrayHsmmSimpleSignalRep1 SimpleSignal skeletal muscle myoblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HSMM Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHrpeSimpleSignalRep2 HRPEpiC 2 HRPEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000389 389 GSM510515 Stam UW hg18 2 wgEncodeUwAffyExonArrayHrpeSimpleSignalRep2 SimpleSignal retinal pigment epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRPEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHrpeSimpleSignalRep1 HRPEpiC 1 HRPEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000389 389 GSM510514 Stam UW hg18 1 wgEncodeUwAffyExonArrayHrpeSimpleSignalRep1 SimpleSignal retinal pigment epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRPEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHrgecSimpleSignalRep2 HRGEC 2 HRGEC AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000832 832 GSM651573 Stam UW 2 wgEncodeUwAffyExonArrayHrgecSimpleSignalRep2 SimpleSignal renal glomerular endothelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRGEC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHrgecSimpleSignalRep1 HRGEC 1 HRGEC AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000832 832 GSM651572 Stam UW 1 wgEncodeUwAffyExonArrayHrgecSimpleSignalRep1 SimpleSignal renal glomerular endothelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRGEC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHreSimpleSignalRep2 HRE 2 HRE AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-06-29 2010-03-29 wgEncodeEH000356 356 GSM472918 Stam UW hg18 2 wgEncodeUwAffyExonArrayHreSimpleSignalRep2 SimpleSignal renal epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRE Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHreSimpleSignalRep1 HRE 1 HRE AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-06-29 2010-03-29 wgEncodeEH000356 356 GSM472919 Stam UW hg18 1 wgEncodeUwAffyExonArrayHreSimpleSignalRep1 SimpleSignal renal epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRE Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHrceSimpleSignalRep2 HRCEpiC 2 HRCEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-06-29 2010-03-29 wgEncodeEH000355 355 GSM472921 Stam UW hg18 2 wgEncodeUwAffyExonArrayHrceSimpleSignalRep2 SimpleSignal renal cortical epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRCEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHrceSimpleSignalRep1 HRCEpiC 1 HRCEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-06-29 2010-03-29 wgEncodeEH000355 355 GSM472920 Stam UW hg18 1 wgEncodeUwAffyExonArrayHrceSimpleSignalRep1 SimpleSignal renal cortical epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HRCEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpfSimpleSignalRep2 HPF 2 HPF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000818 818 GSM580036 Stam UW 2 wgEncodeUwAffyExonArrayHpfSimpleSignalRep2 SimpleSignal pulmonary fibroblasts isolated from lung tissue Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpfSimpleSignalRep1 HPF 1 HPF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000818 818 GSM580035 Stam UW 1 wgEncodeUwAffyExonArrayHpfSimpleSignalRep1 SimpleSignal pulmonary fibroblasts isolated from lung tissue Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpdlfSimpleSignalRep2 HPdLF 2 HPdLF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000819 819 GSM580026 Stam UW 2 wgEncodeUwAffyExonArrayHpdlfSimpleSignalRep2 SimpleSignal periodontal ligament fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPdLF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpdlfSimpleSignalRep1 HPdLF 1 HPdLF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000819 819 GSM580025 Stam UW 1 wgEncodeUwAffyExonArrayHpdlfSimpleSignalRep1 SimpleSignal periodontal ligament fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPdLF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpafSimpleSignalRep2 HPAF 2 HPAF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000817 817 GSM580034 Stam UW 2 wgEncodeUwAffyExonArrayHpafSimpleSignalRep2 SimpleSignal pulmonary artery fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPAF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpafSimpleSignalRep1 HPAF 1 HPAF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000817 817 GSM580033 Stam UW 1 wgEncodeUwAffyExonArrayHpafSimpleSignalRep1 SimpleSignal pulmonary artery fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPAF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHpaecSimpleSignalRep1 HPAEC 1 HPAEC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002158 2158 GSM824860 Stam UW RS19002 1 wgEncodeUwAffyExonArrayHpaecSimpleSignalRep1 SimpleSignal pulmonary artery endothelial cells. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HPAEC Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHnpceSimpleSignalRep2 HNPCEpiC 2 HNPCEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000388 388 GSM510564 Stam UW hg18 2 wgEncodeUwAffyExonArrayHnpceSimpleSignalRep2 SimpleSignal non-pigment ciliary epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HNPCEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHnpceSimpleSignalRep1 HNPCEpiC 1 HNPCEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000388 388 GSM510560 Stam UW hg18 1 wgEncodeUwAffyExonArrayHnpceSimpleSignalRep1 SimpleSignal non-pigment ciliary epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HNPCEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecllySimpleSignalRep2 HMVEC-LLy 2 HMVEC-LLy AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000811 811 GSM580010 Stam UW 2 wgEncodeUwAffyExonArrayHmvecllySimpleSignalRep2 SimpleSignal lymphatic microvascular endothelial cells, lung-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-LLy Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecllySimpleSignalRep1 HMVEC-LLy 1 HMVEC-LLy AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000811 811 GSM580009 Stam UW 1 wgEncodeUwAffyExonArrayHmvecllySimpleSignalRep1 SimpleSignal lymphatic microvascular endothelial cells, lung-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-LLy Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmveclblSimpleSignalRep2 HMVEC-LBl 2 HMVEC-LBl AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000810 810 GSM580020 Stam UW 2 wgEncodeUwAffyExonArrayHmveclblSimpleSignalRep2 SimpleSignal blood microvascular endothelial cells, lung-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-LBl Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmveclblSimpleSignalRep1 HMVEC-LBl 1 HMVEC-LBl AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000810 810 GSM580019 Stam UW 1 wgEncodeUwAffyExonArrayHmveclblSimpleSignalRep1 SimpleSignal blood microvascular endothelial cells, lung-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-LBl Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdneoSimpleSignalRep2 HMVEC-dNeo 2 HMVEC-dNeo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000816 816 GSM580016 Stam UW 2 wgEncodeUwAffyExonArrayHmvecdneoSimpleSignalRep2 SimpleSignal neonatal microvascular endothelial cells (single donor), dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dNeo Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdneoSimpleSignalRep1 HMVEC-dNeo 1 HMVEC-dNeo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000816 816 GSM580015 Stam UW 1 wgEncodeUwAffyExonArrayHmvecdneoSimpleSignalRep1 SimpleSignal neonatal microvascular endothelial cells (single donor), dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dNeo Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdlyneoSimpleSignalRep2 HMVEC-dLy-Neo 2 HMVEC-dLy-Neo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000815 815 GSM580012 Stam UW 2 wgEncodeUwAffyExonArrayHmvecdlyneoSimpleSignalRep2 SimpleSignal neonatal lymphatic microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dLy-Neo Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdlyneoSimpleSignalRep1 HMVEC-dLy-Neo 1 HMVEC-dLy-Neo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000815 815 GSM580011 Stam UW 1 wgEncodeUwAffyExonArrayHmvecdlyneoSimpleSignalRep1 SimpleSignal neonatal lymphatic microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dLy-Neo Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdlyadSimpleSignalRep2 HMVEC-dLy-Ad 2 HMVEC-dLy-Ad AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000814 814 GSM580013 Stam UW 2 wgEncodeUwAffyExonArrayHmvecdlyadSimpleSignalRep2 SimpleSignal adult lymphatic microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dLy-Ad Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdlyadSimpleSignalRep1 HMVEC-dLy-Ad 1 HMVEC-dLy-Ad AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000814 814 GSM580014 Stam UW 1 wgEncodeUwAffyExonArrayHmvecdlyadSimpleSignalRep1 SimpleSignal adult lymphatic microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dLy-Ad Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdblneoSimpleSignalRep2 HMVEC-dBl-Neo 2 HMVEC-dBl-Neo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000813 813 GSM580024 Stam UW 2 wgEncodeUwAffyExonArrayHmvecdblneoSimpleSignalRep2 SimpleSignal neonatal blood microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dBl-Neo Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdblneoSimpleSignalRep1 HMVEC-dBl-Neo 1 HMVEC-dBl-Neo AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000813 813 GSM580023 Stam UW 1 wgEncodeUwAffyExonArrayHmvecdblneoSimpleSignalRep1 SimpleSignal neonatal blood microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dBl-Neo Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdbladSimpleSignalRep2 HMVEC-dBl-Ad 2 HMVEC-dBl-Ad AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000812 812 GSM580022 Stam UW 2 wgEncodeUwAffyExonArrayHmvecdbladSimpleSignalRep2 SimpleSignal adult blood microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dBl-Ad Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdbladSimpleSignalRep1 HMVEC-dBl-Ad 1 HMVEC-dBl-Ad AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000812 812 GSM580021 Stam UW 1 wgEncodeUwAffyExonArrayHmvecdbladSimpleSignalRep1 SimpleSignal adult blood microvascular endothelial cells, dermal-derived Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dBl-Ad Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdadSimpleSignalRep2 HMVEC-dAd 2 HMVEC-dAd AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002157 2157 GSM824852 Stam UW RS19001 2 wgEncodeUwAffyExonArrayHmvecdadSimpleSignalRep2 SimpleSignal adult dermal microvascular endothelial cells. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dAd Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmvecdadSimpleSignalRep1 HMVEC-dAd 1 HMVEC-dAd AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002157 2157 GSM824851 Stam UW RS19000 1 wgEncodeUwAffyExonArrayHmvecdadSimpleSignalRep1 SimpleSignal adult dermal microvascular endothelial cells. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMVEC-dAd Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmfSimpleSignalRep2 HMF 2 HMF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000809 809 GSM580042 Stam UW 2 wgEncodeUwAffyExonArrayHmfSimpleSignalRep2 SimpleSignal mammary fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmfSimpleSignalRep1 HMF 1 HMF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000809 809 GSM580041 Stam UW 1 wgEncodeUwAffyExonArrayHmfSimpleSignalRep1 SimpleSignal mammary fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmecSimpleSignalRep2 HMEC 2 HMEC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000367 367 GSM580006 Stam UW 2 wgEncodeUwAffyExonArrayHmecSimpleSignalRep2 SimpleSignal mammary epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMEC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHmecSimpleSignalRep1 HMEC 1 HMEC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000367 367 GSM472934 Stam UW hg18 1 wgEncodeUwAffyExonArrayHmecSimpleSignalRep1 SimpleSignal mammary epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HMEC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHl60SimpleSignalRep2 HL-60 2 HL-60 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000808 808 GSM472942 Stam UW hg18 2 wgEncodeUwAffyExonArrayHl60SimpleSignalRep2 SimpleSignal promyelocytic leukemia cells, (PMID: 276884) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HL-60 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHl60SimpleSignalRep1 HL-60 1 HL-60 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000808 808 GSM472908 Stam UW hg18 1 wgEncodeUwAffyExonArrayHl60SimpleSignalRep1 SimpleSignal promyelocytic leukemia cells, (PMID: 276884) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HL-60 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHipeSimpleSignalRep2 HIPEpiC 2 HIPEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000387 387 GSM510519 Stam UW hg18 2 wgEncodeUwAffyExonArrayHipeSimpleSignalRep2 SimpleSignal iris pigment epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HIPEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHipeSimpleSignalRep1 HIPEpiC 1 HIPEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000387 387 GSM510518 Stam UW hg18 1 wgEncodeUwAffyExonArrayHipeSimpleSignalRep1 SimpleSignal iris pigment epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HIPEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHgfSimpleSignalRep2 HGF 2 HGF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000807 807 GSM472941 Stam UW hg18 2 wgEncodeUwAffyExonArrayHgfSimpleSignalRep2 SimpleSignal gingival fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HGF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHgfSimpleSignalRep1 HGF 1 HGF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000807 807 GSM472940 Stam UW hg18 1 wgEncodeUwAffyExonArrayHgfSimpleSignalRep1 SimpleSignal gingival fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HGF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHffmycSimpleSignalRep2 HFF-Myc 2 HFF-Myc AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002156 2156 GSM824867 Stam UW RS17570 2 wgEncodeUwAffyExonArrayHffmycSimpleSignalRep2 SimpleSignal foreskin fibroblast cells expressing canine cMyc Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HFF-Myc Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHffmycSimpleSignalRep1 HFF-Myc 1 HFF-Myc AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002156 2156 GSM824866 Stam UW RS17569 1 wgEncodeUwAffyExonArrayHffmycSimpleSignalRep1 SimpleSignal foreskin fibroblast cells expressing canine cMyc Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HFF-Myc Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHffSimpleSignalRep2 HFF 2 HFF AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002155 2155 GSM824865 Stam UW RS17568 2 wgEncodeUwAffyExonArrayHffSimpleSignalRep2 SimpleSignal foreskin fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HFF Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHffSimpleSignalRep1 HFF 1 HFF AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002155 2155 GSM824864 Stam UW RS17567 1 wgEncodeUwAffyExonArrayHffSimpleSignalRep1 SimpleSignal foreskin fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HFF Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHek293SimpleSignalRep2 HEK293 2 HEK293 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000806 806 GSM580028 Stam UW 2 wgEncodeUwAffyExonArrayHek293SimpleSignalRep2 SimpleSignal embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HEK293 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHek293SimpleSignalRep1 HEK293 1 HEK293 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000806 806 GSM580027 Stam UW 1 wgEncodeUwAffyExonArrayHek293SimpleSignalRep1 SimpleSignal embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HEK293 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHeeSimpleSignalRep2 HEEpiC 2 HEEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000386 386 GSM510574 Stam UW hg18 2 wgEncodeUwAffyExonArrayHeeSimpleSignalRep2 SimpleSignal esophageal epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HEEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHeeSimpleSignalRep1 HEEpiC 1 HEEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000386 386 GSM510571 Stam UW hg18 1 wgEncodeUwAffyExonArrayHeeSimpleSignalRep1 SimpleSignal esophageal epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HEEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHct116SimpleSignalRep2 HCT-116 2 HCT-116 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000804 804 GSM580040 Stam UW 2 wgEncodeUwAffyExonArrayHct116SimpleSignalRep2 SimpleSignal colorectal carcinoma (PMID: 7214343) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCT-116 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHct116SimpleSignalRep1 HCT-116 1 HCT-116 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000804 804 GSM580039 Stam UW 1 wgEncodeUwAffyExonArrayHct116SimpleSignalRep1 SimpleSignal colorectal carcinoma (PMID: 7214343) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCT-116 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcpeSimpleSignalRep2 HCPEpiC 2 HCPEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000385 385 GSM510551 Stam UW hg18 2 wgEncodeUwAffyExonArrayHcpeSimpleSignalRep2 SimpleSignal choroid plexus epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCPEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcpeSimpleSignalRep1 HCPEpiC 1 HCPEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000385 385 GSM510547 Stam UW hg18 1 wgEncodeUwAffyExonArrayHcpeSimpleSignalRep1 SimpleSignal choroid plexus epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCPEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHconfSimpleSignalRep2 HConF 2 HConF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000805 805 GSM580008 Stam UW 2 wgEncodeUwAffyExonArrayHconfSimpleSignalRep2 SimpleSignal conjunctival fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HConF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHconfSimpleSignalRep1 HConF 1 HConF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000805 805 GSM580007 Stam UW 1 wgEncodeUwAffyExonArrayHconfSimpleSignalRep1 SimpleSignal conjunctival fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HConF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcmSimpleSignalRep2 HCM 2 HCM AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000384 384 GSM510569 Stam UW hg18 2 wgEncodeUwAffyExonArrayHcmSimpleSignalRep2 SimpleSignal cardiac myocytes Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCM Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcmSimpleSignalRep1 HCM 1 HCM AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000384 384 GSM510566 Stam UW hg18 1 wgEncodeUwAffyExonArrayHcmSimpleSignalRep1 SimpleSignal cardiac myocytes Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCM Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcfaaSimpleSignalRep2 HCFaa 2 HCFaa AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000803 803 GSM580032 Stam UW 2 wgEncodeUwAffyExonArrayHcfaaSimpleSignalRep2 SimpleSignal cardiac fibroblasts- adult atrial Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCFaa Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcfaaSimpleSignalRep1 HCFaa 1 HCFaa AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000803 803 GSM580031 Stam UW 1 wgEncodeUwAffyExonArrayHcfaaSimpleSignalRep1 SimpleSignal cardiac fibroblasts- adult atrial Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCFaa Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcfSimpleSignalRep2 HCF 2 HCF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000383 383 GSM510545 Stam UW hg18 2 wgEncodeUwAffyExonArrayHcfSimpleSignalRep2 SimpleSignal cardiac fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHcfSimpleSignalRep1 HCF 1 HCF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000383 383 GSM510542 Stam UW hg18 1 wgEncodeUwAffyExonArrayHcfSimpleSignalRep1 SimpleSignal cardiac fibroblasts Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HCF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHbvsmcSimpleSignalRep2 HBVSMC 2 HBVSMC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002154 2154 GSM824850 Stam UW RS18999 2 wgEncodeUwAffyExonArrayHbvsmcSimpleSignalRep2 SimpleSignal brain vascular smooth muscle cells. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HBVSMC Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHbvsmcSimpleSignalRep1 HBVSMC 1 HBVSMC AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002154 2154 GSM824849 Stam UW RS18998 1 wgEncodeUwAffyExonArrayHbvsmcSimpleSignalRep1 SimpleSignal brain vascular smooth muscle cells. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HBVSMC Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHbvpSimpleSignalRep1 HBVP 1 HBVP AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002153 2153 GSM824859 Stam UW RS18997 1 wgEncodeUwAffyExonArrayHbvpSimpleSignalRep1 SimpleSignal brain vascular pericytes Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HBVP Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHbmecSimpleSignalRep2 HBMEC 2 HBMEC AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000802 802 GSM651564 Stam UW 2 wgEncodeUwAffyExonArrayHbmecSimpleSignalRep2 SimpleSignal brain microvascular endothelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HBMEC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHbmecSimpleSignalRep1 HBMEC 1 HBMEC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000802 802 GSM580045 Stam UW 1 wgEncodeUwAffyExonArrayHbmecSimpleSignalRep1 SimpleSignal brain microvascular endothelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HBMEC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHaspSimpleSignalRep2 HA-sp 2 HA-sp AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000825 825 GSM651563 Stam UW 2 wgEncodeUwAffyExonArrayHaspSimpleSignalRep2 SimpleSignal astrocytes spinal cord Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HA-sp Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHaspSimpleSignalRep1 HA-sp 1 HA-sp AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000825 825 GSM651562 Stam UW 1 wgEncodeUwAffyExonArrayHaspSimpleSignalRep1 SimpleSignal astrocytes spinal cord Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HA-sp Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHahSimpleSignalRep2 HA-h 2 HA-h AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002152 2152 GSM824863 Stam UW RS17566 2 wgEncodeUwAffyExonArrayHahSimpleSignalRep2 SimpleSignal astrocytes-hippocampal Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HA-h Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHahSimpleSignalRep1 HA-h 1 HA-h AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002152 2152 GSM824862 Stam UW RS17565 1 wgEncodeUwAffyExonArrayHahSimpleSignalRep1 SimpleSignal astrocytes-hippocampal Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HA-h Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHaeSimpleSignalRep2 HAEpiC 2 HAEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000382 382 GSM510517 Stam UW hg18 2 wgEncodeUwAffyExonArrayHaeSimpleSignalRep2 SimpleSignal amniotic epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HAEpiC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHaeSimpleSignalRep1 HAEpiC 1 HAEpiC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000382 382 GSM510516 Stam UW hg18 1 wgEncodeUwAffyExonArrayHaeSimpleSignalRep1 SimpleSignal amniotic epithelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HAEpiC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHacSimpleSignalRep2 HAc 2 HAc AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000831 831 GSM651570 Stam UW 2 wgEncodeUwAffyExonArrayHacSimpleSignalRep2 SimpleSignal astrocytes-cerebellar Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HAc Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHacSimpleSignalRep1 HAc 1 HAc AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000831 831 GSM651569 Stam UW 1 wgEncodeUwAffyExonArrayHacSimpleSignalRep1 SimpleSignal astrocytes-cerebellar Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HAc Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa9dSimpleSignalRep2 H7-hESC 9d 2 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003051 3051 GSM1033349 Stam UW RS16722 2 wgEncodeUwAffyExonArrayH7esDiffa9dSimpleSignalRep2 diffProtA_9d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Simple Signal H7-hESC differentiated 9 d Exon Array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa5dSimpleSignalRep2 H7-hESC 5d 2 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003050 3050 GSM1033347 Stam UW RS16721 2 wgEncodeUwAffyExonArrayH7esDiffa5dSimpleSignalRep2 diffProtA_5d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Simple Signal H7-hESC differentiated 5 d Exon Array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa2dSimpleSignalRep2 H7-hESC 2d 2 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003049 3049 GSM1033352 Stam UW RS16720 2 wgEncodeUwAffyExonArrayH7esDiffa2dSimpleSignalRep2 diffProtA_2d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Simple Signal H7-hESC differentiated 2 d Exon Array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esSimpleSignalRep2 H7-hESC 2 H7-hESC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000381 381 GSM580005 Stam UW 2 wgEncodeUwAffyExonArrayH7esSimpleSignalRep2 SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal H7-hESC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa14dSimpleSignalRep2 H7-hESC 14d 2 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003048 3048 GSM1033350 Stam UW RS16723 2 wgEncodeUwAffyExonArrayH7esDiffa14dSimpleSignalRep2 diffProtA_14d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Simple Signal H7-hESC differentiated 14 d Exon Array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa9dSimpleSignalRep1 H7-hESC 9d 1 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003051 3051 GSM1033348 Stam UW DS15445 1 wgEncodeUwAffyExonArrayH7esDiffa9dSimpleSignalRep1 diffProtA_9d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Simple Signal H7-hESC differentiated 9 d Exon Array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa5dSimpleSignalRep1 H7-hESC 5d 1 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003050 3050 GSM1033346 Stam UW DS15444 1 wgEncodeUwAffyExonArrayH7esDiffa5dSimpleSignalRep1 diffProtA_5d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Simple Signal H7-hESC differentiated 5 d Exon Array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa2dSimpleSignalRep1 H7-hESC 2d 1 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003049 3049 GSM1033353 Stam UW DS15447 1 wgEncodeUwAffyExonArrayH7esDiffa2dSimpleSignalRep1 diffProtA_2d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Simple Signal H7-hESC differentiated 2 d Exon Array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esDiffa14dSimpleSignalRep1 H7-hESC 14d 1 H7-hESC AffyExonArray ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEH003048 3048 GSM1033351 Stam UW DS15446 1 wgEncodeUwAffyExonArrayH7esDiffa14dSimpleSignalRep1 diffProtA_14d SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Simple Signal H7-hESC differentiated 14 d Exon Array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayH7esSimpleSignalRep1 H7-hESC 1 H7-hESC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000381 381 GSM510581 Stam UW hg18 1 wgEncodeUwAffyExonArrayH7esSimpleSignalRep1 SimpleSignal undifferentiated embryonic stem cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal H7-hESC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayGm12865SimpleSignalRep2 GM12865 2 GM12865 AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002151 2151 GSM824874 Stam UW DS12442 2 wgEncodeUwAffyExonArrayGm12865SimpleSignalRep2 SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal GM12865 Exon-array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayGm12865SimpleSignalRep1 GM12865 1 GM12865 AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002151 2151 GSM824873 Stam UW DS12436 1 wgEncodeUwAffyExonArrayGm12865SimpleSignalRep1 SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal GM12865 Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayGm12864SimpleSignalRep1 GM12864 1 GM12864 AffyExonArray ENCODE Mar 2012 Freeze 2011-10-24 2012-07-24 wgEncodeEH002150 2150 GSM824872 Stam UW DS12431 1 wgEncodeUwAffyExonArrayGm12864SimpleSignalRep1 SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal GM12864 Exon-array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayGm06990SimpleSignalRep2 GM06990 2 GM06990 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000360 360 GSM472904 Stam UW hg18 2 wgEncodeUwAffyExonArrayGm06990SimpleSignalRep2 SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal GM06990 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayGm06990SimpleSignalRep1 GM06990 1 GM06990 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000360 360 GSM472903 Stam UW hg18 1 wgEncodeUwAffyExonArrayGm06990SimpleSignalRep1 SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal GM06990 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayCmkSimpleSignalRep1 CMK 1 CMK AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000380 380 GSM510583 Stam UW hg18 1 wgEncodeUwAffyExonArrayCmkSimpleSignalRep1 SimpleSignal acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID: 3016165) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal CMK Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayCaco2SimpleSignalRep2 Caco-2 2 Caco-2 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000359 359 GSM472933 Stam UW hg18 2 wgEncodeUwAffyExonArrayCaco2SimpleSignalRep2 SimpleSignal colorectal adenocarcinoma. (PMID: 1939345) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal Caco-2 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayCaco2SimpleSignalRep1 Caco-2 1 Caco-2 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000359 359 GSM472900 Stam UW hg18 1 wgEncodeUwAffyExonArrayCaco2SimpleSignalRep1 SimpleSignal colorectal adenocarcinoma. (PMID: 1939345) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal Caco-2 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayBjSimpleSignalRep2 BJ 2 BJ AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000365 365 GSM472925 Stam UW hg18 2 wgEncodeUwAffyExonArrayBjSimpleSignalRep2 SimpleSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal BJ Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayBjSimpleSignalRep1 BJ 1 BJ AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000365 365 GSM472924 Stam UW hg18 1 wgEncodeUwAffyExonArrayBjSimpleSignalRep1 SimpleSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal BJ Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayBe2cSimpleSignalRep2 BE2_C 2 BE2_C AffyExonArray ENCODE Mar 2012 Freeze 2011-03-10 2011-12-10 wgEncodeEH000824 824 GSM651568 Stam UW 2 wgEncodeUwAffyExonArrayBe2cSimpleSignalRep2 SimpleSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal BE2_C Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayBe2cSimpleSignalRep1 BE2_C 1 BE2_C AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000824 824 GSM651567 Stam UW 1 wgEncodeUwAffyExonArrayBe2cSimpleSignalRep1 SimpleSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal BE2_C Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAoafSimpleSignalRep2 AoAF 2 AoAF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000801 801 GSM580030 Stam UW 2 wgEncodeUwAffyExonArrayAoafSimpleSignalRep2 SimpleSignal aortic adventitial fibroblast cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AoAF Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAoafSimpleSignalRep1 AoAF 1 AoAF AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000801 801 GSM580029 Stam UW 1 wgEncodeUwAffyExonArrayAoafSimpleSignalRep1 SimpleSignal aortic adventitial fibroblast cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AoAF Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg10803SimpleSignalRep2 AG10803 2 AG10803 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000379 379 GSM510521 Stam UW hg18 2 wgEncodeUwAffyExonArrayAg10803SimpleSignalRep2 SimpleSignal abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG10803 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg10803SimpleSignalRep1 AG10803 1 AG10803 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000379 379 GSM510520 Stam UW hg18 1 wgEncodeUwAffyExonArrayAg10803SimpleSignalRep1 SimpleSignal abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG10803 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg09319SimpleSignalRep2 AG09319 2 AG09319 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000378 378 GSM510538 Stam UW hg18 2 wgEncodeUwAffyExonArrayAg09319SimpleSignalRep2 SimpleSignal gum tissue fibroblasts from apparently heathly 24 year old Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG09319 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg09319SimpleSignalRep1 AG09319 1 AG09319 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000378 378 GSM510536 Stam UW hg18 1 wgEncodeUwAffyExonArrayAg09319SimpleSignalRep1 SimpleSignal gum tissue fibroblasts from apparently heathly 24 year old Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG09319 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg09309SimpleSignalRep2 AG09309 2 AG09309 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2011-05-19 wgEncodeEH000377 377 GSM510525 Stam UW hg18 2 wgEncodeUwAffyExonArrayAg09309SimpleSignalRep2 SimpleSignal adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG09309 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg09309SimpleSignalRep1 AG09309 1 AG09309 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000377 377 GSM510522 Stam UW hg18 1 wgEncodeUwAffyExonArrayAg09309SimpleSignalRep1 SimpleSignal adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG09309 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg04450SimpleSignalRep2 AG04450 2 AG04450 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000376 376 GSM510534 Stam UW hg18 2 wgEncodeUwAffyExonArrayAg04450SimpleSignalRep2 SimpleSignal fetal lung fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG04450 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg04450SimpleSignalRep1 AG04450 1 AG04450 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000376 376 GSM510532 Stam UW hg18 1 wgEncodeUwAffyExonArrayAg04450SimpleSignalRep1 SimpleSignal fetal lung fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG04450 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg04449SimpleSignalRep2 AG04449 2 AG04449 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000375 375 GSM510530 Stam UW hg18 2 wgEncodeUwAffyExonArrayAg04449SimpleSignalRep2 SimpleSignal fetal buttock/thigh fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG04449 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayAg04449SimpleSignalRep1 AG04449 1 AG04449 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000375 375 GSM510528 Stam UW hg18 1 wgEncodeUwAffyExonArrayAg04449SimpleSignalRep1 SimpleSignal fetal buttock/thigh fibroblast Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal AG04449 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayMcf7SimpleSignalRep2 MCF-7 2 MCF-7 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2010-01-10 2010-10-10 wgEncodeEH000370 370 GSM510510 Stam UW hg18 2 wgEncodeUwAffyExonArrayMcf7SimpleSignalRep2 SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal MCF-7 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayMcf7SimpleSignalRep1 MCF-7 1 MCF-7 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000370 370 GSM472936 Stam UW hg18 1 wgEncodeUwAffyExonArrayMcf7SimpleSignalRep1 SimpleSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal MCF-7 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHuvecSimpleSignalRep2 HUVEC 2 HUVEC AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000368 368 GSM651577 Stam UW 2 wgEncodeUwAffyExonArrayHuvecSimpleSignalRep2 SimpleSignal umbilical vein endothelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HUVEC Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHuvecSimpleSignalRep1 HUVEC 1 HUVEC AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000368 368 GSM472935 Stam UW hg18 1 wgEncodeUwAffyExonArrayHuvecSimpleSignalRep1 SimpleSignal umbilical vein endothelial cells Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HUVEC Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHepg2SimpleSignalRep2 HepG2 2 HepG2 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000361 361 GSM472907 Stam UW hg18 2 wgEncodeUwAffyExonArrayHepg2SimpleSignalRep2 SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HepG2 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHepg2SimpleSignalRep1 HepG2 1 HepG2 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000361 361 GSM472906 Stam UW hg18 1 wgEncodeUwAffyExonArrayHepg2SimpleSignalRep1 SimpleSignal hepatocellular carcinoma Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HepG2 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHelas3SimpleSignalRep2 HeLa-S3 2 HeLa-S3 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-06-29 2010-03-29 wgEncodeEH000357 357 GSM472932 Stam UW hg18 2 wgEncodeUwAffyExonArrayHelas3SimpleSignalRep2 SimpleSignal cervical carcinoma Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HeLa-S3 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayHelas3SimpleSignalRep1 HeLa-S3 1 HeLa-S3 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000357 357 GSM472916 Stam UW hg18 1 wgEncodeUwAffyExonArrayHelas3SimpleSignalRep1 SimpleSignal cervical carcinoma Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal HeLa-S3 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayA549SimpleSignalRep2 A549 2 A549 AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000823 823 GSM651561 Stam UW 2 wgEncodeUwAffyExonArrayA549SimpleSignalRep2 SimpleSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal A549 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayA549SimpleSignalRep1 A549 1 A549 AffyExonArray ENCODE Jan 2011 Freeze 2011-01-11 2011-10-10 wgEncodeEH000823 823 GSM651560 Stam UW 1 wgEncodeUwAffyExonArrayA549SimpleSignalRep1 SimpleSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal A549 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayK562SimpleSignalRep2 K562 2 K562 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000362 362 GSM472927 Stam UW hg18 2 wgEncodeUwAffyExonArrayK562SimpleSignalRep2 SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal K562 Exon array Signal Rep 2 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayK562SimpleSignalRep1 K562 1 K562 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-07-02 2010-04-02 wgEncodeEH000362 362 GSM472926 Stam UW hg18 1 wgEncodeUwAffyExonArrayK562SimpleSignalRep1 SimpleSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal K562 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwAffyExonArrayGm12878SimpleSignalRep1 GM12878 1 GM12878 AffyExonArray ENCODE Jan 2011 Freeze 2010-08-19 2009-09-21 2010-06-21 wgEncodeEH000366 366 GSM472931 Stam UW hg18 1 wgEncodeUwAffyExonArrayGm12878SimpleSignalRep1 SimpleSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Affymetrix Exon Microarray Stamatoyannopoulous Stamatoyannopoulous - University of Washington Simple Signal GM12878 Exon array Signal Rep 1 from ENCODE/UW Expression 
wgEncodeUwTfbs UW CTCF Binding GSE30263 None CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington Regulation Description This track was produced as part of the ENCODE Project. This track displays maps of genome-wide binding of the CTCF transcription factor in different cell lines using ChIP-seq high-throughput sequencing. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. For each cell type, this track contains the following views: HotSpots ChIP-seq affinity zones identified using the HotSpot algorithm. Peaks ChIP-seq affinity sites identified as signal peaks within affinity zones (FDR 1.0%). Raw Signal The density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Cells were crosslinked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibodies at 4 &deg;C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross linking in immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. A quantity of 20-50 ng of ChIP DNA was end-repaired, adenine ligated to Illumina adapters was added, and a Solexa library was made for sequencing. ChIP-seq affinity was directly measured through raw tag density (Raw Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). ChIP-seq affinity zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004); 1.0% false discovery rate thresholds (FDR 0.01) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36mers. ChIP-seq affinities (Peaks) were identified as signal peaks within affinity zones (FDR 1.0%) using a peak-finding algorithm. All tracks have a False Discovery Rate of 1% (FDR 1.0%). Verification Data were verified by sequencing biological replicates displaying correlation coefficients &gt; 0.9. Release Notes Release 3 (February 2012) contains 3 new experiments. Credits These data were generated by the UW ENCODE group. Contact: Richard Sandstrom References Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner MO et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUwTfbsViewRawSig Raw Signal CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington Regulation 
wgEncodeUwTfbsWi38InputOhtamStdRawRep1 WI-38 In TAM Sg 1 Input WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002048 2048 GSM1022655 Stam UW DS18351 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsWi38InputOhtamStdRawRep1 4OHTAM_20nM_72hr RawSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 Input OH-tamoxifen 20 nM TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsWi38InputStdRawRep1 WI-38 In Sg 1 Input WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001903 1903 GSM1022647 Stam UW DS18346 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsWi38InputStdRawRep1 None RawSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsWi38CtcfStdRawRep2 WI-38 CTCF Sg 2 CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001902 1902 GSM1022634 Stam UW DS18348 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsWi38CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsWi38CtcfStdRawRep1 WI-38 CTCF Sg 1 CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001902 1902 GSM1022637 Stam UW DS18347 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsWi38CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1InputStdRawRep1 WERI In Sg 1 Input WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000475 475 GSM749766 Stam UW DS11888 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsWerirb1InputStdRawRep1 None RawSignal retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1CtcfStdRawRep2 WERI CTCF Sg 2 CTCF WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-07-02 2010-04-02 wgEncodeEH000402 402 GSM749679 Stam UW DS10408 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsWerirb1CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1CtcfStdRawRep1 WERI CTCF Sg 1 CTCF WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000402 402 GSM749768 Stam UW DS10701 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsWerirb1CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraInputStdRawRep1 SKRA In Sg 1 Input SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000474 474 GSM749700 Stam UW DS11605 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsSknshraInputStdRawRep1 None RawSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraCtcfStdRawRep2 SKRA CTCF Sg 2 CTCF SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000439 439 GSM749667 Stam UW DS12400 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsSknshraCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraCtcfStdRawRep1 SKRA CTCF Sg 1 CTCF SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000439 439 GSM749693 Stam UW DS12399 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsSknshraCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknmcInputStdRawRep1 SKNMC In Sg 1 Input SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001901 1901 GSM1022638 Stam UW DS18341 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsSknmcInputStdRawRep1 None RawSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSkmcInputStdRawRep1 SKMC In Sg 1 Input SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002173 2173 GSM1022646 Stam UW DS16208 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsSkmcInputStdRawRep1 None RawSignal skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SKMC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecInputStdRawRep1 SAEC In Sg 1 Input SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000473 473 GSM749682 Stam UW DS11550 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsSaecInputStdRawRep1 None RawSignal small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecCtcfStdRawRep2 SAEC CTCF Sg 2 CTCF SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000437 437 GSM749779 Stam UW DS12397 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsSaecCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecCtcfStdRawRep1 SAEC CTCF Sg 1 CTCF SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000437 437 GSM749684 Stam UW DS12398 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsSaecCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecInputStdRawRep1 RPTC In Sg 1 Input RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002045 2045 GSM1022642 Stam UW DS18336 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsRptecInputStdRawRep1 None RawSignal renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecCtcfStdRawRep2 RPTC CTCF Sg 2 CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002059 2059 GSM1022666 Stam UW DS18337 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsRptecCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecCtcfStdRawRep1 RPTC CTCF Sg 1 CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002059 2059 GSM1022667 Stam UW DS18338 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsRptecCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsPanc1InputStdRawRep1 PANC In Sg 1 Input PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001900 1900 GSM1022632 Stam UW DS18331 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsPanc1InputStdRawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhlfInputStdRawRep1 NHLF In Sg 1 Input NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001899 1899 GSM1022641 Stam UW DS16347 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsNhlfInputStdRawRep1 None RawSignal lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhlfCtcfStdRawRep1 NHLF CTCF Sg 1 CTCF NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002548 2548 GSM1022626 Stam UW DS16349 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsNhlfCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekInputStdRawRep1 NHEK In Sg 1 Input NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000472 472 GSM749744 Stam UW DS11542 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsNhekInputStdRawRep1 None RawSignal epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekCtcfStdRawRep2 NHEK CTCF Sg 2 CTCF NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000406 406 GSM749747 Stam UW DS11556 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsNhekCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekCtcfStdRawRep1 NHEK CTCF Sg 1 CTCF NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000406 406 GSM749707 Stam UW DS12396 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsNhekCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoInputStdRawRep1 NHDF In Sg 1 Input NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000972 972 GSM749722 Stam UW DS16203 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsNhdfneoInputStdRawRep1 None RawSignal neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoCtcfStdRawRep2 NHDF CTCF Sg 2 CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002058 2058 GSM1022676 Stam UW DS16205 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsNhdfneoCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoCtcfStdRawRep1 NHDF CTCF Sg 1 CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002058 2058 GSM1022675 Stam UW DS16204 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsNhdfneoCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNb4InputStdRawRep1 NB4 In Sg 1 Input NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000970 970 GSM749716 Stam UW DS16344 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsNb4InputStdRawRep1 None RawSignal acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NB4 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNb4CtcfStdRawRep1 NB4 CTCF Sg 1 CTCF NB4 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001898 1898 GSM1022643 Stam UW DS16345 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsNb4CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NB4 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsLncapInputStdRawRep1 LNCP In Sg 1 Input LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001897 1897 GSM1022672 Stam UW DS18326 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsLncapInputStdRawRep1 None RawSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) LNCaP Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsJurkatInputStdRawRep1 Jurk In Sg 1 Input Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000966 966 GSM749672 Stam UW DS16193 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsJurkatInputStdRawRep1 None RawSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfInputStdRawRep1 HVMF In Sg 1 Input HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000964 964 GSM749703 Stam UW DS16190 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHvmfInputStdRawRep1 None RawSignal villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfCtcfStdRawRep2 HVMF CTCF Sg 2 CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002056 2056 GSM1022628 Stam UW DS18572 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHvmfCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfCtcfStdRawRep1 HVMF CTCF Sg 1 CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002056 2056 GSM1022630 Stam UW DS18571 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHvmfCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeInputStdRawRep1 HRpC In Sg 1 Input HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000962 962 GSM749771 Stam UW DS16014 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHrpeInputStdRawRep1 None RawSignal retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpIC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeCtcfStdRawRep2 HRpC CTCF Sg 2 CTCF HRPEpiC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000988 988 GSM1022665 Stam UW DS18570 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHrpeCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpIC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeCtcfStdRawRep1 HRpC CTCF Sg 1 CTCF HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000988 988 GSM749673 Stam UW DS16187 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHrpeCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpIC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreInputStdRawRep1 HRE In Sg 1 Input HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000467 467 GSM749778 Stam UW DS11549 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHreInputStdRawRep1 None RawSignal renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreCtcfStdRawRep2 HRE CTCF Sg 2 CTCF HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-29 2010-06-29 wgEncodeEH000405 405 GSM749737 Stam UW DS11574 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsHreCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreCtcfStdRawRep1 HRE CTCF Sg 1 CTCF HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000405 405 GSM749727 Stam UW DS11572 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHreCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfInputStdRawRep1 HPF In Sg 1 Input HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000960 960 GSM749773 Stam UW DS16180 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHpfInputStdRawRep1 None RawSignal pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfCtcfStdRawRep2 HPF CTCF Sg 2 CTCF HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000987 987 GSM749717 Stam UW DS16182 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHpfCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfCtcfStdRawRep1 HPF CTCF Sg 1 CTCF HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000987 987 GSM749699 Stam UW DS16181 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHpfCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafInputStdRawRep1 HPAF In Sg 1 Input HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000958 958 GSM749709 Stam UW DS16177 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHpafInputStdRawRep1 None RawSignal pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafCtcfStdRawRep2 HPAF CTCF Sg 2 CTCF HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000986 986 GSM749751 Stam UW DS16178 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHpafCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafCtcfStdRawRep1 HPAF CTCF Sg 1 CTCF HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000986 986 GSM749681 Stam UW DS16179 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHpafCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfInputStdRawRep1 HMF In Sg 1 Input HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000956 956 GSM749763 Stam UW DS16174 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHmfInputStdRawRep1 None RawSignal mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfCtcfStdRawRep2 HMF CTCF Sg 2 CTCF HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000985 985 GSM749675 Stam UW DS16175 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHmfCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfCtcfStdRawRep1 HMF CTCF Sg 1 CTCF HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000985 985 GSM749665 Stam UW DS16176 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHmfCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecInputStdRawRep1 HMEC In Sg 1 Input HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000466 466 GSM749755 Stam UW DS13600 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHmecInputStdRawRep1 None RawSignal mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecCtcfStdRawRep2 HMEC CTCF Sg 2 CTCF HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000419 419 GSM1022631 Stam UW DS18569 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHmecCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecCtcfStdRawRep1 HMEC CTCF Sg 1 CTCF HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-12 2010-07-11 wgEncodeEH000419 419 GSM749753 Stam UW DS11255 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHmecCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHl60InputStdRawRep1 HL60 In Sg 1 Input HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000465 465 GSM749775 Stam UW DS13664 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHl60InputStdRawRep1 None RawSignal promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHl60CtcfStdRawRep1 HL60 CTCF Sg 1 CTCF HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000397 397 GSM749688 Stam UW DS9413 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHl60CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycInputStdRawRep1 HFMyc In Sg 1 Input HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001896 1896 GSM1022654 Stam UW DS18321 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHffmycInputStdRawRep1 None RawSignal foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF-Myc Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycCtcfStdRawRep2 HFMyc CTCF Sg 2 CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001895 1895 GSM1022669 Stam UW DS18323 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHffmycCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF-Myc CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycCtcfStdRawRep1 HFMyc CTCF Sg 1 CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001895 1895 GSM1022671 Stam UW DS18322 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHffmycCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF-Myc CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffInputStdRawRep1 HFF In Sg 1 Input HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002043 2043 GSM1022627 Stam UW DS18316 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHffInputStdRawRep1 None RawSignal foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffCtcfStdRawRep1 HFF CTCF Sg 1 CTCF HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002547 2547 GSM1022644 Stam UW DS18318 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHffCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293InputStdRawRep1 H293 In Sg 1 Input HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000464 464 GSM749767 Stam UW DS13603 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHek293InputStdRawRep1 None RawSignal embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEK293 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293CtcfStdRawRep2 H293 CTCF Sg 2 CTCF HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000396 396 GSM749687 Stam UW DS10410 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsHek293CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEK293 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293CtcfStdRawRep1 H293 CTCF Sg 1 CTCF HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000396 396 GSM749668 Stam UW DS10699 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHek293CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEK293 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeInputStdRawRep1 HEpC In Sg 1 Input HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000952 952 GSM749698 Stam UW DS16057 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHeeInputStdRawRep1 None RawSignal esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpIC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeCtcfStdRawRep2 HEpC CTCF Sg 2 CTCF HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000984 984 GSM749726 Stam UW DS16058 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHeeCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpIC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeCtcfStdRawRep1 HEpC CTCF Sg 1 CTCF HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000984 984 GSM749712 Stam UW DS16059 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHeeCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpIC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116InputStdRawRep1 HCT16 In Sg 1 Input HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000950 950 GSM749774 Stam UW DS16013 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHct116InputStdRawRep1 None RawSignal colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116CtcfStdRawRep2 HCT16 CTCF Sg 2 CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002055 2055 GSM1022651 Stam UW DS18568 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHct116CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116CtcfStdRawRep1 HCT16 CTCF Sg 1 CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002055 2055 GSM1022652 Stam UW DS18710 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHct116CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeInputStdRawRep1 HCpC In Sg 1 Input HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000948 948 GSM749776 Stam UW DS15917 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHcpeInputStdRawRep1 None RawSignal choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpIC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeCtcfStdRawRep2 HCpC CTCF Sg 2 CTCF HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000983 983 GSM749745 Stam UW DS16052 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHcpeCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpIC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeCtcfStdRawRep1 HCpC CTCF Sg 1 CTCF HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000983 983 GSM749735 Stam UW DS16051 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHcpeCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpIC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmInputStdRawRep1 HCM In Sg 1 Input HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000946 946 GSM749738 Stam UW DS15916 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHcmInputStdRawRep1 None RawSignal cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmCtcfStdRawRep2 HCM CTCF Sg 2 CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH001894 1894 GSM1022677 Stam UW DS18567 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHcmCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmCtcfStdRawRep1 HCM CTCF Sg 1 CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001894 1894 GSM1022657 Stam UW DS18566 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHcmCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcfaaInputStdRawRep1 HCFa In Sg 1 Input HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000944 944 GSM749761 Stam UW DS15915 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHcfaaInputStdRawRep1 None RawSignal cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCFaa Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcfaaCtcfStdRawRep1 HCFa CTCF Sg 1 CTCF HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000982 982 GSM749732 Stam UW DS16048 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHcfaaCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCFaa CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcfInputStdRawRep1 HCF In Sg 1 Input HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000942 942 GSM749713 Stam UW DS15914 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHcfInputStdRawRep1 None RawSignal cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecInputStdRawRep1 HBMEC In Sg 1 Input HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000940 940 GSM749746 Stam UW DS15913 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHbmecInputStdRawRep1 None RawSignal brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecCtcfStdRawRep2 HBMEC CTCF Sg 2 CTCF HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000981 981 GSM749710 Stam UW DS16047 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHbmecCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecCtcfStdRawRep1 HBMEC CTCF Sg 1 CTCF HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000981 981 GSM749743 Stam UW DS16046 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHbmecCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspInputStdRawRep1 HAsp In Sg 1 Input HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000974 974 GSM749720 Stam UW DS16041 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHaspInputStdRawRep1 None RawSignal astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspCtcfStdRawRep2 HAsp CTCF Sg 2 CTCF HA-sp std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000989 989 GSM1022668 Stam UW DS18987 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHaspCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspCtcfStdRawRep1 HAsp CTCF Sg 1 CTCF HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000989 989 GSM749696 Stam UW DS16042 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHaspCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacInputStdRawRep1 HAc In Sg 1 Input HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002165 2165 GSM1022673 Stam UW DS18311 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsHacInputStdRawRep1 None RawSignal astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacCtcfStdRawRep2 HAc CTCF Sg 2 CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH001893 1893 GSM1022662 Stam UW DS18312 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsHacCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacCtcfStdRawRep1 HAc CTCF Sg 1 CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001893 1893 GSM1022661 Stam UW DS18313 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsHacCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsH7esInputStdRawRep1 H7 In Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002532 2532 GSM1022649 Stam UW DS14111 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsH7esInputStdRawRep1 diffProtA_14d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-HESC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsH7esInputStdDiffa9dRawRep1 H7 In 9d Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002545 2545 GSM1022660 Stam UW DS15393 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsH7esInputStdDiffa9dRawRep1 diffProtA_9d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-HESC Input diffProtA 9d TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsH7esInputStdDiffa5dRawRep1 H7 In 5d Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002544 2544 GSM1022656 Stam UW DS14110 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsH7esInputStdDiffa5dRawRep1 diffProtA_5d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-HESC Input diffProtA 5d TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsH7esInputStdDiffa2dRawRep1 H7 In 2d Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002543 2543 GSM1022670 Stam UW DS15392 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsH7esInputStdDiffa2dRawRep1 diffProtA_2d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-HESC Input diffProtA 2d TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875InputStdRawRep1 GM75 In Sg 1 Input GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-16 2011-03-15 wgEncodeEH000462 462 GSM749724 Stam UW DS13589 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12875InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12875 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875CtcfStdRawRep2 GM75 CTCF Sg 2 CTCF GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000452 452 GSM749670 Stam UW DS11899 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12875CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12875 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875CtcfStdRawRep1 GM75 CTCF Sg 1 CTCF GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000452 452 GSM749764 Stam UW DS10993 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12875CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12875 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874InputStdRawRep1 GM74 In Sg 1 Input GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000461 461 GSM749742 Stam UW DS13588 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12874InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12874 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874CtcfStdRawRep2 GM74 CTCF Sg 2 CTCF GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000451 451 GSM749741 Stam UW DS10992 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12874CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12874 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874CtcfStdRawRep1 GM74 CTCF Sg 1 CTCF GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000451 451 GSM749757 Stam UW DS11503 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12874CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12874 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873InputStdRawRep1 GM73 In Sg 1 Input GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000460 460 GSM749685 Stam UW DS13586 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12873InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12873 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdRawRep3 GM73 CTCF Sg 3 CTCF GM12873 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000450 450 GSM1022629 Stam UW DS14433 WindowDensity-bin20-win+/-75 hg19 3 exp wgEncodeUwTfbsGm12873CtcfStdRawRep3 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12873 CTCF TFBS ChIP-seq Raw Signal 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdRawRep2 GM73 CTCF Sg 2 CTCF GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000450 450 GSM749686 Stam UW DS11501 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12873CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12873 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdRawRep1 GM73 CTCF Sg 1 CTCF GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000450 450 GSM749730 Stam UW DS10990 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12873CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12873 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872InputStdRawRep1 GM72 In Sg 1 Input GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000459 459 GSM749765 Stam UW DS13585 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12872InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12872 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdRawRep3 GM72 CTCF Sg 3 CTCF GM12872 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000449 449 GSM1022633 Stam UW DS14432 WindowDensity-bin20-win+/-75 hg19 3 exp wgEncodeUwTfbsGm12872CtcfStdRawRep3 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12872 CTCF TFBS ChIP-seq Raw Signal 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdRawRep2 GM72 CTCF Sg 2 CTCF GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000449 449 GSM749692 Stam UW DS11500 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12872CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12872 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdRawRep1 GM72 CTCF Sg 1 CTCF GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000449 449 GSM749694 Stam UW DS10989 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12872CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12872 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865InputStdRawRep1 GM65 In Sg 1 Input GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000458 458 GSM749777 Stam UW DS13590 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12865InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdRawRep3 GM65 CTCF Sg 3 CTCF GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000448 448 GSM1022636 Stam UW DS13756 WindowDensity-bin20-win+/-75 hg19 3 exp wgEncodeUwTfbsGm12865CtcfStdRawRep3 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 CTCF TFBS ChIP-seq Raw Signal 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdRawRep2 GM65 CTCF Sg 2 CTCF GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000448 448 GSM749725 Stam UW DS10991 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12865CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdRawRep1 GM65 CTCF Sg 1 CTCF GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000448 448 GSM749740 Stam UW DS11502 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12865CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864InputStdRawRep1 GM64 In Sg 1 Input GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000457 457 GSM749754 Stam UW DS13587 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12864InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdRawRep3 GM64 CTCF Sg 3 CTCF GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000447 447 GSM1022664 Stam UW DS14431 WindowDensity-bin20-win+/-75 hg19 3 exp wgEncodeUwTfbsGm12864CtcfStdRawRep3 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 CTCF TFBS ChIP-seq Raw Signal 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdRawRep2 GM64 CTCF Sg 2 CTCF GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000447 447 GSM749762 Stam UW DS11499 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12864CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdRawRep1 GM64 CTCF Sg 1 CTCF GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000447 447 GSM749676 Stam UW DS10988 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12864CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12801InputStdRawRep1 GM01 In Sg 1 Input GM12801 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000456 456 GSM749701 Stam UW DS13665 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12801InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12801 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12801CtcfStdRawRep1 GM01 CTCF Sg 1 CTCF GM12801 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000393 393 GSM749711 Stam UW DS8755 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12801CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12801 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990InputStdRawRep1 GM90 In Sg 1 Input GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000455 455 GSM749731 Stam UW DS11497 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm06990InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990CtcfStdRawRep2 GM90 CTCF Sg 2 CTCF GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-21 2010-06-20 wgEncodeEH000392 392 GSM749705 Stam UW DS11520 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm06990CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990CtcfStdRawRep1 GM90 CTCF Sg 1 CTCF GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-29 2010-03-29 wgEncodeEH000392 392 GSM749708 Stam UW DS11518 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm06990CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2InputStdRawRep1 Caco2 In Sg 1 Input Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000454 454 GSM749691 Stam UW DS13597 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsCaco2InputStdRawRep1 None RawSignal colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2CtcfStdRawRep2 Caco2 CTCF Sg 2 CTCF Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-20 2010-06-20 wgEncodeEH000404 404 GSM749689 Stam UW DS11674 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsCaco2CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2CtcfStdRawRep1 Caco2 CTCF Sg 1 CTCF Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-20 2010-06-20 wgEncodeEH000404 404 GSM749748 Stam UW DS11675 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsCaco2CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjInputStdRawRep1 BJ In Sg 1 Input BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000453 453 GSM749770 Stam UW DS11544 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsBjInputStdRawRep1 None RawSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjCtcfStdRawRep2 BJ CTCF Sg 2 CTCF BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-20 2010-06-19 wgEncodeEH000403 403 GSM749752 Stam UW DS11562 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsBjCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjCtcfStdRawRep1 BJ CTCF Sg 1 CTCF BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-20 2010-06-20 wgEncodeEH000403 403 GSM749677 Stam UW DS11560 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsBjCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cInputStdRawRep1 BE2c In Sg 1 Input BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001892 1892 GSM1022648 Stam UW DS18306 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsBe2cInputStdRawRep1 None RawSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2c Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cCtcfStdRawRep2 BE2c CTCF Sg 2 CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001891 1891 GSM1022650 Stam UW DS18308 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsBe2cCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2c CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cCtcfStdRawRep1 BE2c CTCF Sg 1 CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001891 1891 GSM1022653 Stam UW DS18307 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsBe2cCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2c CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafInputStdRawRep1 AoAF In Sg 1 Input AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000938 938 GSM749772 Stam UW DS15912 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsAoafInputStdRawRep1 None RawSignal aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafCtcfStdRawRep2 AoAF CTCF Sg 2 CTCF AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000980 980 GSM749736 Stam UW DS16039 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsAoafCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafCtcfStdRawRep1 AoAF CTCF Sg 1 CTCF AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000980 980 GSM749666 Stam UW DS16040 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsAoafCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803InputStdRawRep1 AG03 In Sg 1 Input AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000936 936 GSM749734 Stam UW DS15911 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsAg10803InputStdRawRep1 None RawSignal abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803CtcfStdRawRep2 AG03 CTCF Sg 2 CTCF AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000979 979 GSM749759 Stam UW DS16038 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsAg10803CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803CtcfStdRawRep1 AG03 CTCF Sg 1 CTCF AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000979 979 GSM749714 Stam UW DS16037 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsAg10803CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319InputStdRawRep1 AG19 In Sg 1 Input AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000934 934 GSM749671 Stam UW DS15910 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsAg09319InputStdRawRep1 None RawSignal gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319CtcfStdRawRep2 AG19 CTCF Sg 2 CTCF AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000978 978 GSM749723 Stam UW DS16036 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsAg09319CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319CtcfStdRawRep1 AG19 CTCF Sg 1 CTCF AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000978 978 GSM749728 Stam UW DS16035 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsAg09319CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309InputStdRawRep1 AG09 In Sg 1 Input AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000932 932 GSM749718 Stam UW DS16030 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsAg09309InputStdRawRep1 None RawSignal adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309CtcfStdRawRep2 AG09 CTCF Sg 2 CTCF AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000977 977 GSM749680 Stam UW DS16031 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsAg09309CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309CtcfStdRawRep1 AG09 CTCF Sg 1 CTCF AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000977 977 GSM749750 Stam UW DS16032 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsAg09309CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450InputStdRawRep1 AG50 In Sg 1 Input AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000930 930 GSM749697 Stam UW DS15909 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsAg04450InputStdRawRep1 None RawSignal fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450CtcfStdRawRep2 AG50 CTCF Sg 2 CTCF AG04450 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH000976 976 GSM1022635 Stam UW DS18603 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsAg04450CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450CtcfStdRawRep1 AG50 CTCF Sg 1 CTCF AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000976 976 GSM749769 Stam UW DS16029 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsAg04450CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449InputStdRawRep1 AG49 In Sg 1 Input AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000928 928 GSM749702 Stam UW DS15908 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsAg04449InputStdRawRep1 None RawSignal fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449CtcfStdRawRep2 AG49 CTCF Sg 2 CTCF AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000975 975 GSM749678 Stam UW DS15736 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsAg04449CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449CtcfStdRawRep1 AG49 CTCF Sg 1 CTCF AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000975 975 GSM749695 Stam UW DS15738 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsAg04449CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsMonocd14ro1746InputStdRawRep1 CD14+ In Sg 1 Input Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002169 2169 GSM1022659 Stam UW DS18980 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsMonocd14ro1746InputStdRawRep1 None RawSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Monocytes-CD14+ RO1746 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7InputStdRawRep1 MCF7 In Sg 1 Input MCF-7 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000968 968 GSM749760 Stam UW DS16198 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsMcf7InputStdRawRep1 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7CtcfStdRawRep2 MCF7 CTCF Sg 2 CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002057 2057 GSM1022663 Stam UW DS16199 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsMcf7CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7CtcfStdRawRep1 MCF7 CTCF Sg 1 CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002057 2057 GSM1022658 Stam UW DS16200 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsMcf7CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecInputStdRawRep1 HUVEC In Sg 1 Input HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000468 468 GSM749758 Stam UW DS11470 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHuvecInputStdRawRep1 None RawSignal umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecCtcfStdRawRep2 HUVEC CTCF Sg 2 CTCF HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000410 410 GSM749749 Stam UW DS11457 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsHuvecCtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecCtcfStdRawRep1 HUVEC CTCF Sg 1 CTCF HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-29 2010-06-29 wgEncodeEH000410 410 GSM749674 Stam UW DS12395 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHuvecCtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2InputStdRawRep1 HepG2 In Sg 1 Input HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000470 470 GSM749756 Stam UW DS13599 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHepg2InputStdRawRep1 None RawSignal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2CtcfStdRawRep2 HepG2 CTCF Sg 2 CTCF HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000401 401 GSM749683 Stam UW DS11677 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsHepg2CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2CtcfStdRawRep1 HepG2 CTCF Sg 1 CTCF HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000401 401 GSM749715 Stam UW DS10700 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHepg2CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3InputStdRawRep1 HeLaS3 In Sg 1 Input HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000469 469 GSM749721 Stam UW DS11540 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsHelas3InputStdRawRep1 None RawSignal cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3CtcfStdRawRep2 HeLaS3 CTCF Sg 2 CTCF HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-21 wgEncodeEH000398 398 GSM749739 Stam UW DS11167 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsHelas3CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3CtcfStdRawRep1 HeLaS3 CTCF Sg 1 CTCF HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000398 398 GSM749729 Stam UW DS11552 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsHelas3CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsCd20ro01794InputStdRawRep1 CD20+94 In Sg 1 Input CD20+_RO01794 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEH002172 2172 GSM1022645 Stam UW DS18982 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsCd20ro01794InputStdRawRep1 None RawSignal B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ RO01794 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsCd20ro01778InputStdRawRep1 CD20+78 In Sg 1 Input CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-25 wgEncodeEH002170 2170 GSM1022625 Stam UW DS18984 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsCd20ro01778InputStdRawRep1 None RawSignal B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ RO01778 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549InputStdRawRep1 A549 In Sg 1 Input A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH001904 1904 GSM1022674 Stam UW DS18301 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwTfbsA549InputStdRawRep1 None RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549CtcfStdRawRep2 A549 CTCF Sg 2 CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001890 1890 GSM1022639 Stam UW DS18302 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwTfbsA549CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549CtcfStdRawRep1 A549 CTCF Sg 1 CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001890 1890 GSM1022640 Stam UW DS18303 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwTfbsA549CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562InputStdRawRep1 K562 In Sg 1 Input K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000471 471 GSM749719 Stam UW DS11488 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsK562InputStdRawRep1 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562CtcfStdRawRep2 K562 CTCF Sg 2 CTCF K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-21 2010-06-20 wgEncodeEH000399 399 GSM749733 Stam UW DS11508 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsK562CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562CtcfStdRawRep1 K562 CTCF Sg 1 CTCF K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-30 2010-03-29 wgEncodeEH000399 399 GSM749690 Stam UW DS11247 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsK562CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878InputStdRawRep1 GM78 In Sg 1 Input GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000463 463 GSM749669 Stam UW DS11883 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwTfbsGm12878InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Input TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878CtcfStdRawRep2 GM78 CTCF Sg 2 CTCF GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-21 2010-06-20 wgEncodeEH000394 394 GSM749706 Stam UW DS11165 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwTfbsGm12878CtcfStdRawRep2 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 CTCF TFBS ChIP-seq Raw Signal 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878CtcfStdRawRep1 GM78 CTCF Sg 1 CTCF GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-06-30 2010-03-29 wgEncodeEH000394 394 GSM749704 Stam UW DS11510 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwTfbsGm12878CtcfStdRawRep1 None RawSignal CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsViewPeaks Peaks CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington Regulation 
wgEncodeUwTfbsWi38CtcfStdPkRep2 WI-38 CTCF Pk 2 CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001902 1902 GSM1022634 Stam UW DS18348 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsWi38CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WI-38 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsWi38CtcfStdPkRep1 WI-38 CTCF Pk 1 CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001902 1902 GSM1022637 Stam UW DS18347 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsWi38CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WI-38 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1CtcfStdPkRep2 WERI CTCF Pk 2 CTCF WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-07-02 2010-04-02 wgEncodeEH000402 402 GSM749679 Stam UW DS10408 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsWerirb1CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WERI-Rb-1 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1CtcfStdPkRep1 WERI CTCF Pk 1 CTCF WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000402 402 GSM749768 Stam UW DS10701 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsWerirb1CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WERI-Rb-1 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraCtcfStdPkRep2 SKRA CTCF Pk 2 CTCF SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000439 439 GSM749667 Stam UW DS12400 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsSknshraCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraCtcfStdPkRep1 SKRA CTCF Pk 1 CTCF SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000439 439 GSM749693 Stam UW DS12399 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsSknshraCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecCtcfStdPkRep2 SAEC CTCF Pk 2 CTCF SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000437 437 GSM749779 Stam UW DS12397 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsSaecCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecCtcfStdPkRep1 SAEC CTCF Pk 1 CTCF SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000437 437 GSM749684 Stam UW DS12398 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsSaecCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecCtcfStdPkRep2 RPTC CTCF Pk 2 CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002059 2059 GSM1022666 Stam UW DS18337 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsRptecCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPTEC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecCtcfStdPkRep1 RPTC CTCF Pk 1 CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002059 2059 GSM1022667 Stam UW DS18338 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsRptecCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPTEC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhlfCtcfStdPkRep1 NHLF CTCF Pk 1 CTCF NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002548 2548 GSM1022626 Stam UW DS16349 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsNhlfCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHLF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekCtcfStdPkRep2 NHEK CTCF Pk 2 CTCF NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000406 406 GSM749747 Stam UW DS11556 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsNhekCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekCtcfStdPkRep1 NHEK CTCF Pk 1 CTCF NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000406 406 GSM749707 Stam UW DS12396 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsNhekCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoCtcfStdPkRep2 NHDF CTCF Pk 2 CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002058 2058 GSM1022676 Stam UW DS16205 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsNhdfneoCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-neo CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoCtcfStdPkRep1 NHDF CTCF Pk 1 CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002058 2058 GSM1022675 Stam UW DS16204 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsNhdfneoCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-neo CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNb4CtcfStdPkRep1 NB4 CTCF Pk 1 CTCF NB4 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001898 1898 GSM1022643 Stam UW DS16345 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsNb4CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NB4 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfCtcfStdPkRep2 HVMF CTCF Pk 2 CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002056 2056 GSM1022628 Stam UW DS18572 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHvmfCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HVMF CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfCtcfStdPkRep1 HVMF CTCF Pk 1 CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002056 2056 GSM1022630 Stam UW DS18571 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHvmfCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HVMF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeCtcfStdPkRep2 HRpC CTCF Pk 2 CTCF HRPEpiC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000988 988 GSM1022665 Stam UW DS18570 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHrpeCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRPEpIC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeCtcfStdPkRep1 HRpC CTCF Pk 1 CTCF HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000988 988 GSM749673 Stam UW DS16187 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHrpeCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRPEpIC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreCtcfStdPkRep2 HRE CTCF Pk 2 CTCF HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000405 405 GSM749737 Stam UW DS11574 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsHreCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreCtcfStdPkRep1 HRE CTCF Pk 1 CTCF HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000405 405 GSM749727 Stam UW DS11572 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHreCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfCtcfStdPkRep2 HPF CTCF Pk 2 CTCF HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000987 987 GSM749717 Stam UW DS16182 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHpfCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfCtcfStdPkRep1 HPF CTCF Pk 1 CTCF HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000987 987 GSM749699 Stam UW DS16181 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHpfCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafCtcfStdPkRep2 HPAF CTCF Pk 2 CTCF HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000986 986 GSM749751 Stam UW DS16178 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHpafCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafCtcfStdPkRep1 HPAF CTCF Pk 1 CTCF HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000986 986 GSM749681 Stam UW DS16179 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHpafCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfCtcfStdPkRep2 HMF CTCF Pk 2 CTCF HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000985 985 GSM749675 Stam UW DS16175 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHmfCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfCtcfStdPkRep1 HMF CTCF Pk 1 CTCF HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000985 985 GSM749665 Stam UW DS16176 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHmfCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecCtcfStdPkRep2 HMEC CTCF Pk 2 CTCF HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000419 419 GSM1022631 Stam UW DS18569 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHmecCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecCtcfStdPkRep1 HMEC CTCF Pk 1 CTCF HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-12 2010-07-11 wgEncodeEH000419 419 GSM749753 Stam UW DS11255 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHmecCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHl60CtcfStdPkRep1 HL60 CTCF Pk 1 CTCF HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000397 397 GSM749688 Stam UW DS9413 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHl60CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HL-60 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycCtcfStdPkRep2 HFMyc CTCF Pk 2 CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001895 1895 GSM1022669 Stam UW DS18323 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHffmycCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF-Myc CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycCtcfStdPkRep1 HFMyc CTCF Pk 1 CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001895 1895 GSM1022671 Stam UW DS18322 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHffmycCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF-Myc CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffCtcfStdPkRep1 HFF CTCF Pk 1 CTCF HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002547 2547 GSM1022644 Stam UW DS18318 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHffCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293CtcfStdPkRep2 H293 CTCF Pk 2 CTCF HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000396 396 GSM749687 Stam UW DS10410 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsHek293CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEK293 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293CtcfStdPkRep1 H293 CTCF Pk 1 CTCF HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000396 396 GSM749668 Stam UW DS10699 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHek293CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEK293 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeCtcfStdPkRep2 HEpC CTCF Pk 2 CTCF HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000984 984 GSM749726 Stam UW DS16058 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHeeCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEEpIC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeCtcfStdPkRep1 HEpC CTCF Pk 1 CTCF HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000984 984 GSM749712 Stam UW DS16059 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHeeCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEEpIC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116CtcfStdPkRep2 HCT16 CTCF Pk 2 CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002055 2055 GSM1022651 Stam UW DS18568 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHct116CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCT-116 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116CtcfStdPkRep1 HCT16 CTCF Pk 1 CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002055 2055 GSM1022652 Stam UW DS18710 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHct116CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCT-116 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeCtcfStdPkRep2 HCpC CTCF Pk 2 CTCF HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000983 983 GSM749745 Stam UW DS16052 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHcpeCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpIC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeCtcfStdPkRep1 HCpC CTCF Pk 1 CTCF HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000983 983 GSM749735 Stam UW DS16051 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHcpeCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpIC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmCtcfStdPkRep2 HCM CTCF Pk 2 CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH001894 1894 GSM1022677 Stam UW DS18567 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHcmCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCM CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmCtcfStdPkRep1 HCM CTCF Pk 1 CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001894 1894 GSM1022657 Stam UW DS18566 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHcmCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCM CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcfaaCtcfStdPkRep1 HCFa CTCF Pk 1 CTCF HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000982 982 GSM749732 Stam UW DS16048 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHcfaaCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCFaa CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecCtcfStdPkRep2 HBMEC CTCF Pk 2 CTCF HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000981 981 GSM749710 Stam UW DS16047 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHbmecCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBMEC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecCtcfStdPkRep1 HBMEC CTCF Pk 1 CTCF HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000981 981 GSM749743 Stam UW DS16046 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHbmecCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBMEC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspCtcfStdPkRep2 HAsp CTCF Pk 2 CTCF HA-sp std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000989 989 GSM1022668 Stam UW DS18987 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHaspCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-sp CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspCtcfStdPkRep1 HAsp CTCF Pk 1 CTCF HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000989 989 GSM749696 Stam UW DS16042 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHaspCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-sp CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacCtcfStdPkRep2 HAc CTCF Pk 2 CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH001893 1893 GSM1022662 Stam UW DS18312 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsHacCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAc CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacCtcfStdPkRep1 HAc CTCF Pk 1 CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001893 1893 GSM1022661 Stam UW DS18313 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsHacCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAc CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875CtcfStdPkRep2 GM75 CTCF Pk 2 CTCF GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-16 2011-03-15 wgEncodeEH000452 452 GSM749670 Stam UW DS11899 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12875CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12875 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875CtcfStdPkRep1 GM75 CTCF Pk 1 CTCF GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000452 452 GSM749764 Stam UW DS10993 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12875CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12875 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874CtcfStdPkRep2 GM74 CTCF Pk 2 CTCF GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-06-08 2011-03-07 wgEncodeEH000451 451 GSM749741 Stam UW DS10992 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12874CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12874 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874CtcfStdPkRep1 GM74 CTCF Pk 1 CTCF GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000451 451 GSM749757 Stam UW DS11503 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12874CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12874 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdPkRep3 GM73 CTCF Pk 3 CTCF GM12873 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000450 450 GSM1022629 Stam UW DS14433 lmax-v1.0 hg19 3 exp wgEncodeUwTfbsGm12873CtcfStdPkRep3 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12873 CTCF TFBS ChIP-seq Peaks 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdPkRep2 GM73 CTCF Pk 2 CTCF GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000450 450 GSM749686 Stam UW DS11501 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12873CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12873 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdPkRep1 GM73 CTCF Pk 1 CTCF GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000450 450 GSM749730 Stam UW DS10990 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12873CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12873 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdPkRep3 GM72 CTCF Pk 3 CTCF GM12872 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000449 449 GSM1022633 Stam UW DS14432 lmax-v1.0 hg19 3 exp wgEncodeUwTfbsGm12872CtcfStdPkRep3 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12872 CTCF TFBS ChIP-seq Peaks 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdPkRep2 GM72 CTCF Pk 2 CTCF GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-06-08 2011-03-07 wgEncodeEH000449 449 GSM749692 Stam UW DS11500 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12872CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12872 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdPkRep1 GM72 CTCF Pk 1 CTCF GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000449 449 GSM749694 Stam UW DS10989 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12872CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12872 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdPkRep3 GM65 CTCF Pk 3 CTCF GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000448 448 GSM1022636 Stam UW DS13756 lmax-v1.0 hg19 3 exp wgEncodeUwTfbsGm12865CtcfStdPkRep3 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 CTCF TFBS ChIP-seq Peaks 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdPkRep2 GM65 CTCF Pk 2 CTCF GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-06-08 2011-03-07 wgEncodeEH000448 448 GSM749725 Stam UW DS10991 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12865CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdPkRep1 GM65 CTCF Pk 1 CTCF GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000448 448 GSM749740 Stam UW DS11502 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12865CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdPkRep3 GM64 CTCF Pk 3 CTCF GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000447 447 GSM1022664 Stam UW DS14431 lmax-v1.0 hg19 3 exp wgEncodeUwTfbsGm12864CtcfStdPkRep3 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 CTCF TFBS ChIP-seq Peaks 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdPkRep2 GM64 CTCF Pk 2 CTCF GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-06-08 2011-03-07 wgEncodeEH000447 447 GSM749762 Stam UW DS11499 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12864CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdPkRep1 GM64 CTCF Pk 1 CTCF GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000447 447 GSM749676 Stam UW DS10988 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12864CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12801CtcfStdPkRep1 GM01 CTCF Pk 1 CTCF GM12801 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000393 393 GSM749711 Stam UW DS8755 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12801CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12801 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990CtcfStdPkRep2 GM90 CTCF Pk 2 CTCF GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-29 2010-03-29 wgEncodeEH000392 392 GSM749705 Stam UW DS11520 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm06990CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990CtcfStdPkRep1 GM90 CTCF Pk 1 CTCF GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-29 2010-03-29 wgEncodeEH000392 392 GSM749708 Stam UW DS11518 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm06990CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2CtcfStdPkRep2 Caco2 CTCF Pk 2 CTCF Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-06-08 2011-03-07 wgEncodeEH000404 404 GSM749689 Stam UW DS11674 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsCaco2CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2CtcfStdPkRep1 Caco2 CTCF Pk 1 CTCF Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-20 2010-06-20 wgEncodeEH000404 404 GSM749748 Stam UW DS11675 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsCaco2CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjCtcfStdPkRep2 BJ CTCF Pk 2 CTCF BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2010-06-07 2011-03-07 wgEncodeEH000403 403 GSM749752 Stam UW DS11562 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsBjCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjCtcfStdPkRep1 BJ CTCF Pk 1 CTCF BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-20 2010-06-20 wgEncodeEH000403 403 GSM749677 Stam UW DS11560 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsBjCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cCtcfStdPkRep2 BE2c CTCF Pk 2 CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001891 1891 GSM1022650 Stam UW DS18308 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsBe2cCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BE2c CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cCtcfStdPkRep1 BE2c CTCF Pk 1 CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001891 1891 GSM1022653 Stam UW DS18307 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsBe2cCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BE2c CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafCtcfStdPkRep2 AoAF CTCF Pk 2 CTCF AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000980 980 GSM749736 Stam UW DS16039 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsAoafCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafCtcfStdPkRep1 AoAF CTCF Pk 1 CTCF AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000980 980 GSM749666 Stam UW DS16040 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsAoafCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803CtcfStdPkRep2 AG03 CTCF Pk 2 CTCF AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000979 979 GSM749759 Stam UW DS16038 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsAg10803CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG10803 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803CtcfStdPkRep1 AG03 CTCF Pk 1 CTCF AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000979 979 GSM749714 Stam UW DS16037 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsAg10803CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG10803 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319CtcfStdPkRep2 AG19 CTCF Pk 2 CTCF AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000978 978 GSM749723 Stam UW DS16036 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsAg09319CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09319 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319CtcfStdPkRep1 AG19 CTCF Pk 1 CTCF AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000978 978 GSM749728 Stam UW DS16035 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsAg09319CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09319 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309CtcfStdPkRep2 AG09 CTCF Pk 2 CTCF AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000977 977 GSM749680 Stam UW DS16031 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsAg09309CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09309 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309CtcfStdPkRep1 AG09 CTCF Pk 1 CTCF AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000977 977 GSM749750 Stam UW DS16032 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsAg09309CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09309 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450CtcfStdPkRep2 AG50 CTCF Pk 2 CTCF AG04450 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH000976 976 GSM1022635 Stam UW DS18603 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsAg04450CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450CtcfStdPkRep1 AG50 CTCF Pk 1 CTCF AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000976 976 GSM749769 Stam UW DS16029 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsAg04450CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449CtcfStdPkRep2 AG49 CTCF Pk 2 CTCF AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000975 975 GSM749678 Stam UW DS15736 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsAg04449CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04449 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449CtcfStdPkRep1 AG49 CTCF Pk 1 CTCF AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000975 975 GSM749695 Stam UW DS15738 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsAg04449CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04449 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7CtcfStdPkRep2 MCF7 CTCF Pk 2 CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002057 2057 GSM1022663 Stam UW DS16199 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsMcf7CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7CtcfStdPkRep1 MCF7 CTCF Pk 1 CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002057 2057 GSM1022658 Stam UW DS16200 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsMcf7CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecCtcfStdPkRep2 HUVEC CTCF Pk 2 CTCF HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000410 410 GSM749749 Stam UW DS11457 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsHuvecCtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecCtcfStdPkRep1 HUVEC CTCF Pk 1 CTCF HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-29 2010-06-29 wgEncodeEH000410 410 GSM749674 Stam UW DS12395 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHuvecCtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2CtcfStdPkRep2 HepG2 CTCF Pk 2 CTCF HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000401 401 GSM749683 Stam UW DS11677 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsHepg2CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2CtcfStdPkRep1 HepG2 CTCF Pk 1 CTCF HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000401 401 GSM749715 Stam UW DS10700 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHepg2CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3CtcfStdPkRep2 HeLaS3 CTCF Pk 2 CTCF HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000398 398 GSM749739 Stam UW DS11167 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsHelas3CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3CtcfStdPkRep1 HeLaS3 CTCF Pk 1 CTCF HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000398 398 GSM749729 Stam UW DS11552 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsHelas3CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549CtcfStdPkRep2 A549 CTCF Pk 2 CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001890 1890 GSM1022639 Stam UW DS18302 lmax-v1.0 hg19 2 exp wgEncodeUwTfbsA549CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment A549 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549CtcfStdPkRep1 A549 CTCF Pk 1 CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001890 1890 GSM1022640 Stam UW DS18303 lmax-v1.0 hg19 1 exp wgEncodeUwTfbsA549CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment A549 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562CtcfStdPkRep2 K562 CTCF Pk 2 CTCF K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-06-30 2010-03-29 wgEncodeEH000399 399 GSM749733 Stam UW DS11508 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsK562CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562CtcfStdPkRep1 K562 CTCF Pk 1 CTCF K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-30 2010-03-29 wgEncodeEH000399 399 GSM749690 Stam UW DS11247 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsK562CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878CtcfStdPkRep2 GM78 CTCF Pk 2 CTCF GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-06-30 2010-03-29 wgEncodeEH000394 394 GSM749706 Stam UW DS11165 lmax-v1.0 hg18 2 exp wgEncodeUwTfbsGm12878CtcfStdPkRep2 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 CTCF TFBS ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878CtcfStdPkRep1 GM78 CTCF Pk 1 CTCF GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-29 2010-03-29 wgEncodeEH000394 394 GSM749704 Stam UW DS11510 lmax-v1.0 hg18 1 exp wgEncodeUwTfbsGm12878CtcfStdPkRep1 None Peaks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 CTCF TFBS ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsViewHot Hotspots CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington Regulation 
wgEncodeUwTfbsWi38CtcfStdHotspotsRep2 WI-38 CTCF Ht 2 CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001902 1902 GSM1022634 Stam UW DS18348 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsWi38CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsWi38CtcfStdHotspotsRep1 WI-38 CTCF Ht 1 CTCF WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001902 1902 GSM1022637 Stam UW DS18347 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsWi38CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1CtcfStdHotspotsRep2 WERI CTCF Ht 2 CTCF WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-07-02 2010-04-02 wgEncodeEH000402 402 GSM749679 Stam UW DS10408 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsWerirb1CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WERI-Rb-1 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsWerirb1CtcfStdHotspotsRep1 WERI CTCF Ht 1 CTCF WERI-Rb-1 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000402 402 GSM749768 Stam UW DS10701 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsWerirb1CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WERI-Rb-1 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraCtcfStdHotspotsRep2 SKRA CTCF Ht 2 CTCF SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000439 439 GSM749667 Stam UW DS12400 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsSknshraCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsSknshraCtcfStdHotspotsRep1 SKRA CTCF Ht 1 CTCF SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000439 439 GSM749693 Stam UW DS12399 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsSknshraCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecCtcfStdHotspotsRep2 SAEC CTCF Ht 2 CTCF SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000437 437 GSM749779 Stam UW DS12397 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsSaecCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsSaecCtcfStdHotspotsRep1 SAEC CTCF Ht 1 CTCF SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000437 437 GSM749684 Stam UW DS12398 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsSaecCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecCtcfStdHotspotsRep2 RPTC CTCF Ht 2 CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002059 2059 GSM1022666 Stam UW DS18337 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsRptecCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm RPTEC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsRptecCtcfStdHotspotsRep1 RPTC CTCF Ht 1 CTCF RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002059 2059 GSM1022667 Stam UW DS18338 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsRptecCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm RPTEC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhlfCtcfStdHotspotsRep1 NHLF CTCF Ht 1 CTCF NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002548 2548 GSM1022626 Stam UW DS16349 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsNhlfCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHLF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekCtcfStdHotspotsRep2 NHEK CTCF Ht 2 CTCF NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000406 406 GSM749747 Stam UW DS11556 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsNhekCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhekCtcfStdHotspotsRep1 NHEK CTCF Ht 1 CTCF NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000406 406 GSM749707 Stam UW DS12396 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsNhekCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoCtcfStdHotspotsRep2 NHDF CTCF Ht 2 CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002058 2058 GSM1022676 Stam UW DS16205 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsNhdfneoCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-neo CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsNhdfneoCtcfStdHotspotsRep1 NHDF CTCF Ht 1 CTCF NHDF-neo std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002058 2058 GSM1022675 Stam UW DS16204 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsNhdfneoCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-neo CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsNb4CtcfStdHotspotsRep1 NB4 CTCF Ht 1 CTCF NB4 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001898 1898 GSM1022643 Stam UW DS16345 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsNb4CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NB4 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfCtcfStdHotspotsRep2 HVMF CTCF Ht 2 CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002056 2056 GSM1022628 Stam UW DS18572 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHvmfCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HVMF CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHvmfCtcfStdHotspotsRep1 HVMF CTCF Ht 1 CTCF HVMF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002056 2056 GSM1022630 Stam UW DS18571 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsHvmfCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HVMF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeCtcfStdHotspotsRep2 HRpC CTCF Ht 2 CTCF HRPEpiC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000988 988 GSM1022665 Stam UW DS18570 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHrpeCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRPEpIC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHrpeCtcfStdHotspotsRep1 HRpC CTCF Ht 1 CTCF HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000988 988 GSM749673 Stam UW DS16187 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHrpeCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRPEpIC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreCtcfStdHotspotsRep2 HRE CTCF Ht 2 CTCF HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-29 2010-06-29 wgEncodeEH000405 405 GSM749737 Stam UW DS11574 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsHreCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHreCtcfStdHotspotsRep1 HRE CTCF Ht 1 CTCF HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-20 wgEncodeEH000405 405 GSM749727 Stam UW DS11572 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHreCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfCtcfStdHotspotsRep2 HPF CTCF Ht 2 CTCF HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000987 987 GSM749717 Stam UW DS16182 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsHpfCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPF CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpfCtcfStdHotspotsRep1 HPF CTCF Ht 1 CTCF HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000987 987 GSM749699 Stam UW DS16181 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHpfCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafCtcfStdHotspotsRep2 HPAF CTCF Ht 2 CTCF HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000986 986 GSM749751 Stam UW DS16178 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsHpafCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPAF CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHpafCtcfStdHotspotsRep1 HPAF CTCF Ht 1 CTCF HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000986 986 GSM749681 Stam UW DS16179 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHpafCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPAF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfCtcfStdHotspotsRep2 HMF CTCF Ht 2 CTCF HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000985 985 GSM749675 Stam UW DS16175 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsHmfCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMF CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmfCtcfStdHotspotsRep1 HMF CTCF Ht 1 CTCF HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000985 985 GSM749665 Stam UW DS16176 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHmfCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecCtcfStdHotspotsRep2 HMEC CTCF Ht 2 CTCF HMEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000419 419 GSM1022631 Stam UW DS18569 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHmecCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMEC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHmecCtcfStdHotspotsRep1 HMEC CTCF Ht 1 CTCF HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-12 2010-07-11 wgEncodeEH000419 419 GSM749753 Stam UW DS11255 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHmecCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMEC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHl60CtcfStdHotspotsRep1 HL60 CTCF Ht 1 CTCF HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000397 397 GSM749688 Stam UW DS9413 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHl60CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HL-60 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycCtcfStdHotspotsRep2 HFMyc CTCF Ht 2 CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001895 1895 GSM1022669 Stam UW DS18323 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHffmycCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFF-Myc CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffmycCtcfStdHotspotsRep1 HFMyc CTCF Ht 1 CTCF HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001895 1895 GSM1022671 Stam UW DS18322 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsHffmycCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFF-Myc CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHffCtcfStdHotspotsRep1 HFF CTCF Ht 1 CTCF HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002547 2547 GSM1022644 Stam UW DS18318 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsHffCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293CtcfStdHotspotsRep2 H293 CTCF Ht 2 CTCF HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000396 396 GSM749687 Stam UW DS10410 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsHek293CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEK293 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHek293CtcfStdHotspotsRep1 H293 CTCF Ht 1 CTCF HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000396 396 GSM749668 Stam UW DS10699 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHek293CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEK293 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeCtcfStdHotspotsRep2 HEpC CTCF Ht 2 CTCF HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000984 984 GSM749726 Stam UW DS16058 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsHeeCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEEpIC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHeeCtcfStdHotspotsRep1 HEpC CTCF Ht 1 CTCF HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000984 984 GSM749712 Stam UW DS16059 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHeeCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEEpIC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116CtcfStdHotspotsRep2 HCT16 CTCF Ht 2 CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002055 2055 GSM1022651 Stam UW DS18568 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHct116CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCT-116 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHct116CtcfStdHotspotsRep1 HCT16 CTCF Ht 1 CTCF HCT-116 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002055 2055 GSM1022652 Stam UW DS18710 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsHct116CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCT-116 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeCtcfStdHotspotsRep2 HCpC CTCF Ht 2 CTCF HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000983 983 GSM749745 Stam UW DS16052 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsHcpeCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCPEpIC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcpeCtcfStdHotspotsRep1 HCpC CTCF Ht 1 CTCF HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000983 983 GSM749735 Stam UW DS16051 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHcpeCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCPEpIC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmCtcfStdHotspotsRep2 HCM CTCF Ht 2 CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH001894 1894 GSM1022677 Stam UW DS18567 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHcmCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCM CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcmCtcfStdHotspotsRep1 HCM CTCF Ht 1 CTCF HCM std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001894 1894 GSM1022657 Stam UW DS18566 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsHcmCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCM CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHcfaaCtcfStdHotspotsRep1 HCFa CTCF Ht 1 CTCF HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000982 982 GSM749732 Stam UW DS16048 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHcfaaCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCFaa CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecCtcfStdHotspotsRep2 HBMEC CTCF Ht 2 CTCF HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000981 981 GSM749710 Stam UW DS16047 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsHbmecCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBMEC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHbmecCtcfStdHotspotsRep1 HBMEC CTCF Ht 1 CTCF HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000981 981 GSM749743 Stam UW DS16046 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHbmecCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBMEC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspCtcfStdHotspotsRep2 HAsp CTCF Ht 2 CTCF HA-sp std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000989 989 GSM1022668 Stam UW DS18987 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHaspCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HA-sp CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHaspCtcfStdHotspotsRep1 HAsp CTCF Ht 1 CTCF HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000989 989 GSM749696 Stam UW DS16042 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsHaspCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HA-sp CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacCtcfStdHotspotsRep2 HAc CTCF Ht 2 CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH001893 1893 GSM1022662 Stam UW DS18312 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsHacCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAc CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHacCtcfStdHotspotsRep1 HAc CTCF Ht 1 CTCF HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001893 1893 GSM1022661 Stam UW DS18313 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsHacCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAc CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875CtcfStdHotspotsRep2 GM75 CTCF Ht 2 CTCF GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000452 452 GSM749670 Stam UW DS11899 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12875CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12875 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12875CtcfStdHotspotsRep1 GM75 CTCF Ht 1 CTCF GM12875 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000452 452 GSM749764 Stam UW DS10993 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12875CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12875 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874CtcfStdHotspotsRep2 GM74 CTCF Ht 2 CTCF GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000451 451 GSM749741 Stam UW DS10992 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12874CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12874 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12874CtcfStdHotspotsRep1 GM74 CTCF Ht 1 CTCF GM12874 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000451 451 GSM749757 Stam UW DS11503 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12874CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12874 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdHotspotsRep3 GM73 CTCF Ht 3 CTCF GM12873 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000450 450 GSM1022629 Stam UW DS14433 Hotspot-v5.2 hg19 3 exp wgEncodeUwTfbsGm12873CtcfStdHotspotsRep3 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12873 CTCF TFBS ChIP-seq Hotspots 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdHotspotsRep2 GM73 CTCF Ht 2 CTCF GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000450 450 GSM749686 Stam UW DS11501 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12873CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12873 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12873CtcfStdHotspotsRep1 GM73 CTCF Ht 1 CTCF GM12873 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-01-11 2010-10-11 wgEncodeEH000450 450 GSM749730 Stam UW DS10990 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12873CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12873 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdHotspotsRep3 GM72 CTCF Ht 3 CTCF GM12872 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000449 449 GSM1022633 Stam UW DS14432 Hotspot-v5.2 hg19 3 exp wgEncodeUwTfbsGm12872CtcfStdHotspotsRep3 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12872 CTCF TFBS ChIP-seq Hotspots 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdHotspotsRep2 GM72 CTCF Ht 2 CTCF GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000449 449 GSM749692 Stam UW DS11500 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12872CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12872 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12872CtcfStdHotspotsRep1 GM72 CTCF Ht 1 CTCF GM12872 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000449 449 GSM749694 Stam UW DS10989 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12872CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12872 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdHotspotsRep3 GM65 CTCF Ht 3 CTCF GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000448 448 GSM1022636 Stam UW DS13756 Hotspot-v5.2 hg19 3 exp wgEncodeUwTfbsGm12865CtcfStdHotspotsRep3 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 CTCF TFBS ChIP-seq Hotspots 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdHotspotsRep2 GM65 CTCF Ht 2 CTCF GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000448 448 GSM749725 Stam UW DS10991 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12865CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12865CtcfStdHotspotsRep1 GM65 CTCF Ht 1 CTCF GM12865 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000448 448 GSM749740 Stam UW DS11502 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12865CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdHotspotsRep3 GM64 CTCF Ht 3 CTCF GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000447 447 GSM1022664 Stam UW DS14431 Hotspot-v5.2 hg19 3 exp wgEncodeUwTfbsGm12864CtcfStdHotspotsRep3 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12864 CTCF TFBS ChIP-seq Hotspots 3 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdHotspotsRep2 GM64 CTCF Ht 2 CTCF GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000447 447 GSM749762 Stam UW DS11499 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12864CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12864 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12864CtcfStdHotspotsRep1 GM64 CTCF Ht 1 CTCF GM12864 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2010-01-11 2010-10-11 wgEncodeEH000447 447 GSM749676 Stam UW DS10988 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12864CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12864 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12801CtcfStdHotspotsRep1 GM01 CTCF Ht 1 CTCF GM12801 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000393 393 GSM749711 Stam UW DS8755 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12801CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12801 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990CtcfStdHotspotsRep2 GM90 CTCF Ht 2 CTCF GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-21 2010-06-20 wgEncodeEH000392 392 GSM749705 Stam UW DS11520 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm06990CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm06990CtcfStdHotspotsRep1 GM90 CTCF Ht 1 CTCF GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-29 2010-03-29 wgEncodeEH000392 392 GSM749708 Stam UW DS11518 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm06990CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2CtcfStdHotspotsRep2 Caco2 CTCF Ht 2 CTCF Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-20 2010-06-20 wgEncodeEH000404 404 GSM749689 Stam UW DS11674 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsCaco2CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsCaco2CtcfStdHotspotsRep1 Caco2 CTCF Ht 1 CTCF Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-09-20 2010-06-20 wgEncodeEH000404 404 GSM749748 Stam UW DS11675 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsCaco2CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjCtcfStdHotspotsRep2 BJ CTCF Ht 2 CTCF BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-20 2010-06-19 wgEncodeEH000403 403 GSM749752 Stam UW DS11562 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsBjCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsBjCtcfStdHotspotsRep1 BJ CTCF Ht 1 CTCF BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-20 2010-06-20 wgEncodeEH000403 403 GSM749677 Stam UW DS11560 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsBjCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cCtcfStdHotspotsRep2 BE2c CTCF Ht 2 CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001891 1891 GSM1022650 Stam UW DS18308 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsBe2cCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BE2c CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsBe2cCtcfStdHotspotsRep1 BE2c CTCF Ht 1 CTCF BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001891 1891 GSM1022653 Stam UW DS18307 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsBe2cCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BE2c CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafCtcfStdHotspotsRep2 AoAF CTCF Ht 2 CTCF AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000980 980 GSM749736 Stam UW DS16039 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsAoafCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AoAF CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAoafCtcfStdHotspotsRep1 AoAF CTCF Ht 1 CTCF AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000980 980 GSM749666 Stam UW DS16040 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsAoafCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AoAF CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803CtcfStdHotspotsRep2 AG03 CTCF Ht 2 CTCF AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000979 979 GSM749759 Stam UW DS16038 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsAg10803CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG10803 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg10803CtcfStdHotspotsRep1 AG03 CTCF Ht 1 CTCF AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000979 979 GSM749714 Stam UW DS16037 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsAg10803CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG10803 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319CtcfStdHotspotsRep2 AG19 CTCF Ht 2 CTCF AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000978 978 GSM749723 Stam UW DS16036 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsAg09319CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09319 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09319CtcfStdHotspotsRep1 AG19 CTCF Ht 1 CTCF AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000978 978 GSM749728 Stam UW DS16035 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsAg09319CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09319 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309CtcfStdHotspotsRep2 AG09 CTCF Ht 2 CTCF AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000977 977 GSM749680 Stam UW DS16031 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsAg09309CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09309 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg09309CtcfStdHotspotsRep1 AG09 CTCF Ht 1 CTCF AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000977 977 GSM749750 Stam UW DS16032 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsAg09309CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09309 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450CtcfStdHotspotsRep2 AG50 CTCF Ht 2 CTCF AG04450 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH000976 976 GSM1022635 Stam UW DS18603 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsAg04450CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04450CtcfStdHotspotsRep1 AG50 CTCF Ht 1 CTCF AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000976 976 GSM749769 Stam UW DS16029 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsAg04450CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449CtcfStdHotspotsRep2 AG49 CTCF Ht 2 CTCF AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000975 975 GSM749678 Stam UW DS15736 Hotspot-v5.1 hg19 2 exp wgEncodeUwTfbsAg04449CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04449 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsAg04449CtcfStdHotspotsRep1 AG49 CTCF Ht 1 CTCF AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000975 975 GSM749695 Stam UW DS15738 Hotspot-v5.1 hg19 1 exp wgEncodeUwTfbsAg04449CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04449 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7CtcfStdHotspotsRep2 MCF7 CTCF Ht 2 CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002057 2057 GSM1022663 Stam UW DS16199 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsMcf7CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsMcf7CtcfStdHotspotsRep1 MCF7 CTCF Ht 1 CTCF MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002057 2057 GSM1022658 Stam UW DS16200 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsMcf7CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecCtcfStdHotspotsRep2 HUVEC CTCF Ht 2 CTCF HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000410 410 GSM749749 Stam UW DS11457 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsHuvecCtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHuvecCtcfStdHotspotsRep1 HUVEC CTCF Ht 1 CTCF HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-29 2010-06-29 wgEncodeEH000410 410 GSM749674 Stam UW DS12395 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHuvecCtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2CtcfStdHotspotsRep2 HepG2 CTCF Ht 2 CTCF HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000401 401 GSM749683 Stam UW DS11677 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsHepg2CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHepg2CtcfStdHotspotsRep1 HepG2 CTCF Ht 1 CTCF HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-07-02 2010-04-02 wgEncodeEH000401 401 GSM749715 Stam UW DS10700 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHepg2CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3CtcfStdHotspotsRep2 HeLaS3 CTCF Ht 2 CTCF HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-09-21 2010-06-21 wgEncodeEH000398 398 GSM749739 Stam UW DS11167 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsHelas3CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsHelas3CtcfStdHotspotsRep1 HeLaS3 CTCF Ht 1 CTCF HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-06-30 2010-03-29 wgEncodeEH000398 398 GSM749729 Stam UW DS11552 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsHelas3CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549CtcfStdHotspotsRep2 A549 CTCF Ht 2 CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001890 1890 GSM1022639 Stam UW DS18302 Hotspot-v5.2 hg19 2 exp wgEncodeUwTfbsA549CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm A549 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsA549CtcfStdHotspotsRep1 A549 CTCF Ht 1 CTCF A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001890 1890 GSM1022640 Stam UW DS18303 Hotspot-v5.2 hg19 1 exp wgEncodeUwTfbsA549CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm A549 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562CtcfStdHotspotsRep2 K562 CTCF Ht 2 CTCF K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-21 2010-06-20 wgEncodeEH000399 399 GSM749733 Stam UW DS11508 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsK562CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsK562CtcfStdHotspotsRep1 K562 CTCF Ht 1 CTCF K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-08 2009-06-30 2010-03-29 wgEncodeEH000399 399 GSM749690 Stam UW DS11247 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsK562CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878CtcfStdHotspotsRep2 GM78 CTCF Ht 2 CTCF GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-09-21 2010-06-20 wgEncodeEH000394 394 GSM749706 Stam UW DS11165 Hotspot-v5.1 hg18 2 exp wgEncodeUwTfbsGm12878CtcfStdHotspotsRep2 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 CTCF TFBS ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwTfbsGm12878CtcfStdHotspotsRep1 GM78 CTCF Ht 1 CTCF GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-07 2009-06-30 2010-03-29 wgEncodeEH000394 394 GSM749704 Stam UW DS11510 Hotspot-v5.1 hg18 1 exp wgEncodeUwTfbsGm12878CtcfStdHotspotsRep1 None Hotspots CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 CTCF TFBS ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistone UW Histone GSE35583 Histone Modifications by ChIP-seq from ENCODE/University of Washington Regulation Description This track was produced as part of the ENCODE Project. This track displays genome-wide maps of histone modifications in different cell lines using ChIP-seq high-throughput sequencing. Display Conventions and Configuration This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. For each cell type, this track contains the following views: HotSpots ChIP-seq affinity zones identified using the HotSpot algorithm. Peaks ChIP-seq affinity sites identified as signal peaks within FDR 1.0% affinity zones. Raw Signal The density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown according to the approved ENCODE cell culture protocols. Cells were cross-linked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using a Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibodies at 4 &#176;C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross-linking in the immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. A quantity of 20-50 ng of ChIP DNA was end-repaired, followed by addition of adenine, ligation to Illumina adapters, and creation of a Solexa library for sequencing. ChIP-seq affinity was directly measured through the raw tag density (Raw Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). ChIP-seq affinity zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). One percent false discovery rate thresholds (FDR 1.0%) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36-mers. ChIP-Seq affinities (Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm. All tracks have a False Discovery Rate of 1% (FDR 1.0%). Verification Data were verified by sequencing biological replicates displaying a correlation coefficient greater than 0.9. Release Notes Release 5 (July 2012) of this track removes experiments with K562/Zinc finger knockouts and adds in some missing inputs. Credits These data were generated by the UW ENCODE group. Contact: Richard Sandstrom References Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner MO et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. Data Release Policy Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here. 
wgEncodeUwHistoneViewRawSig Sg Signal Histone Modifications by ChIP-seq from ENCODE/University of Washington Regulation 
wgEncodeUwHistoneWi38InputStdRawRep1 WI38 In Sg 1 Input WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001903 1903 GSM945245 Stam UW DS18346 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneWi38InputStdRawRep1 None RawSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38InputOhtamStdRawRep1 WI38 In Sg 1 Input WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002048 2048 GSM945223 Stam UW DS18351 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneWi38InputOhtamStdRawRep1 4OHTAM_20nM_72hr RawSignal embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 Input 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3StdRawRep2 WI38 H3K4M3 Sg 2 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001914 1914 GSM945265 Stam UW DS18349 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneWi38H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3StdRawRep1 WI38 H3K4M3 Sg 1 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001914 1914 GSM945265 Stam UW DS18350 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneWi38H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3OhtamStdRawRep2 WI38 H3K4M3 Sg 2 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002047 2047 GSM945215 Stam UW DS18354 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneWi38H3k04me3OhtamStdRawRep2 4OHTAM_20nM_72hr RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 H3K4me3 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3OhtamStdRawRep1 WI38 H3K4M3 Sg 1 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002047 2047 GSM945215 Stam UW DS18355 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneWi38H3k04me3OhtamStdRawRep1 4OHTAM_20nM_72hr RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) WI-38 H3K4me3 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1InputStdRawRep1 WERI In Sg 1 Input WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH000475 475 GSM945318 Stam UW DS11888 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneWerirb1InputStdRawRep1 None RawSignal retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1H3k04me3StdRawRep2 WERI H3K4M3 Sg 2 H3K4me3 WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001913 1913 GSM945263 Stam UW DS16213 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneWerirb1H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1H3k04me3StdRawRep1 WERI H3K4M3 Sg 1 H3K4me3 WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001913 1913 GSM945263 Stam UW DS16214 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneWerirb1H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) WERI-Rb-1 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraInputStdRawRep1 SKRA In Sg 1 Input SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000474 474 GSM945317 Stam UW DS11605 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneSknshraInputStdRawRep1 None RawSignal neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k36me3StdRawRep2 SKRA H3K36M3 Sg 2 H3K36me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000441 441 GSM945209 Stam UW DS12403 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneSknshraH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k36me3StdRawRep1 SKRA H3K36M3 Sg 1 H3K36me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000441 441 GSM945209 Stam UW DS12404 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneSknshraH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k27me3StdRawRep2 SKRA H3K27M3 Sg 2 H3K27me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-20 2010-07-20 wgEncodeEH000440 440 GSM945210 Stam UW DS12215 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneSknshraH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k27me3StdRawRep1 SKRA H3K27M3 Sg 1 H3K27me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000440 440 GSM945210 Stam UW DS12212 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneSknshraH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k4me3StdRawRep2 SKRA H3K4M3 Sg 2 H3K4me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000422 422 GSM945202 Stam UW DS11783 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneSknshraH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k4me3StdRawRep1 SKRA H3K4M3 Sg 1 H3K4me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000422 422 GSM945202 Stam UW DS11782 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneSknshraH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-SH_RA H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcInputStdRawRep1 SKNMC In Sg 1 Input SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001901 1901 GSM945247 Stam UW DS18341 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneSknmcInputStdRawRep1 None RawSignal neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcH3k04me3StdRawRep2 SKNMC H3K4M3 Sg 2 H3K4me3 SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001912 1912 GSM945264 Stam UW DS18345 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneSknmcH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcH3k04me3StdRawRep1 SKNMC H3K4M3 Sg 1 H3K4me3 SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001912 1912 GSM945264 Stam UW DS18344 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneSknmcH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SK-N-MC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcInputStdRawRep1 SKMC In Sg 1 Input SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEH002173 2173 GSM945161 Stam UW DS16208 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneSkmcInputStdRawRep1 None RawSignal skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SKMC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcH3k04me3StdRawRep2 SKMC H3K4M3 Sg 2 H3K4me3 SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002046 2046 GSM945214 Stam UW DS16212 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneSkmcH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SKMC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcH3k04me3StdRawRep1 SKMC H3K4M3 Sg 1 H3K4me3 SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002046 2046 GSM945214 Stam UW DS16211 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneSkmcH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SKMC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecInputStdRawRep1 SAEC In Sg 1 Input SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000473 473 GSM945314 Stam UW DS11550 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneSaecInputStdRawRep1 None RawSignal small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k36me3StdRawRep2 SAEC H3K36M3 Sg 2 H3K36me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000438 438 GSM945226 Stam UW DS12246 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneSaecH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k36me3StdRawRep1 SAEC H3K36M3 Sg 1 H3K36me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000438 438 GSM945226 Stam UW DS12243 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneSaecH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k27me3StdRawRep2 SAEC H3K27M3 Sg 2 H3K27me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000420 420 GSM945200 Stam UW DS12245 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneSaecH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k27me3StdRawRep1 SAEC H3K27M3 Sg 1 H3K27me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000420 420 GSM945200 Stam UW DS12242 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneSaecH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k4me3StdRawRep2 SAEC H3K4M3 Sg 2 H3K4me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000421 421 GSM945199 Stam UW DS11579 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneSaecH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k4me3StdRawRep1 SAEC H3K4M3 Sg 1 H3K4me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000421 421 GSM945199 Stam UW DS11577 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneSaecH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) SAEC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecInputStdRawRep1 RPTEC In Sg 1 Input RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002045 2045 GSM945217 Stam UW DS18336 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneRptecInputStdRawRep1 None RawSignal renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecH3k04me3StdRawRep2 RPTEC H3K4M3 Sg 2 H3K4me3 RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002044 2044 GSM945216 Stam UW DS18339 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneRptecH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecH3k04me3StdRawRep1 RPTEC H3K4M3 Sg 1 H3K4me3 RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002044 2044 GSM945216 Stam UW DS18340 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneRptecH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) RPTEC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1InputStdRawRep1 PANC1 In Sg 1 Input PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001900 1900 GSM945246 Stam UW DS18331 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistonePanc1InputStdRawRep1 None RawSignal pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1H3k04me3StdRawRep2 PANC1 H3K4M3 Sg 2 H3K4me3 PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001911 1911 GSM945261 Stam UW DS18334 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistonePanc1H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1H3k04me3StdRawRep1 PANC1 H3K4M3 Sg 1 H3K4me3 PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001911 1911 GSM945261 Stam UW DS18335 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistonePanc1H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) PANC-1 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfInputStdRawRep1 NHLF In Sg 1 Input NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001899 1899 GSM945280 Stam UW DS16347 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneNhlfInputStdRawRep1 None RawSignal lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfH3k04me3StdRawRep2 NHLF H3K4M3 Sg 2 H3K4me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001910 1910 GSM945262 Stam UW DS16350 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneNhlfH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfH3k04me3StdRawRep1 NHLF H3K4M3 Sg 1 H3K4me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001910 1910 GSM945262 Stam UW DS16351 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneNhlfH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHLF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekInputStdRawRep1 NHEK In Sg 1 Input NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000472 472 GSM945313 Stam UW DS11542 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneNhekInputStdRawRep1 None RawSignal epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k36me3StdRawRep2 NHEK H3K36M3 Sg 2 H3K36me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000414 414 GSM945174 Stam UW DS12240 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneNhekH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k36me3StdRawRep1 NHEK H3K36M3 Sg 1 H3K36me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000414 414 GSM945174 Stam UW DS12237 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneNhekH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k27me3StdRawRep2 NHEK H3K27M3 Sg 2 H3K27me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000436 436 GSM945300 Stam UW DS12080 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneNhekH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k27me3StdRawRep1 NHEK H3K27M3 Sg 1 H3K27me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000436 436 GSM945300 Stam UW DS12078 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneNhekH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k4me3StdRawRep2 NHEK H3K4M3 Sg 2 H3K4me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-13 2010-07-12 wgEncodeEH000415 415 GSM945175 Stam UW DS11557 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneNhekH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k4me3StdRawRep1 NHEK H3K4M3 Sg 1 H3K4me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000415 415 GSM945175 Stam UW DS11559 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneNhekH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHEK H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoInputStdRawRep1 NHDF In Sg 1 Input NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000972 972 GSM945250 Stam UW DS16203 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneNhdfneoInputStdRawRep1 None RawSignal neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoH3k4me3StdRawRep2 NHDF H3K4M3 Sg 2 H3K4me3 NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000971 971 GSM945251 Stam UW DS16207 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneNhdfneoH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoH3k4me3StdRawRep1 NHDF H3K4M3 Sg 1 H3K4me3 NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000971 971 GSM945251 Stam UW DS16206 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneNhdfneoH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NHDF-neo H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNb4InputStdRawRep1 NB4 In Sg 1 Input NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000970 970 GSM945252 Stam UW DS16344 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneNb4InputStdRawRep1 None RawSignal acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NB4 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNb4H3k4me3StdRawRep1 NB4 H3K4M3 Sg 1 H3K4me3 NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000969 969 GSM945275 Stam UW DS16346 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneNb4H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) NB4 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapInputStdRawRep1 LNCP In Sg 1 Input LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001897 1897 GSM945282 Stam UW DS18326 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneLncapInputStdRawRep1 None RawSignal prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) LNCaP Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapH3k04me3StdRawRep2 LNCP H3K4M3 Sg 2 H3K4me3 LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001909 1909 GSM945240 Stam UW DS18329 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneLncapH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) LNCaP H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapH3k04me3StdRawRep1 LNCP H3K4M3 Sg 1 H3K4me3 LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001909 1909 GSM945240 Stam UW DS18330 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneLncapH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) LNCaP H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatInputStdRawRep1 Jurk In Sg 1 Input Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000966 966 GSM945268 Stam UW DS16193 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneJurkatInputStdRawRep1 None RawSignal T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatH3k4me3StdRawRep2 Jurk H3K4M3 Sg 2 H3K4me3 Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000965 965 GSM945267 Stam UW DS16196 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneJurkatH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatH3k4me3StdRawRep1 Jurk H3K4M3 Sg 1 H3K4me3 Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000965 965 GSM945267 Stam UW DS16197 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneJurkatH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Jurkat H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfInputStdRawRep1 HVMF In Sg 1 Input HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000964 964 GSM945266 Stam UW DS16190 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHvmfInputStdRawRep1 None RawSignal villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfH3k4me3StdRawRep2 HVMF H3K4M3 Sg 2 H3K4me3 HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000963 963 GSM945273 Stam UW DS16155 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHvmfH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfH3k4me3StdRawRep1 HVMF H3K4M3 Sg 1 H3K4me3 HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000963 963 GSM945273 Stam UW DS16156 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHvmfH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HVMF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeInputStdRawRep1 HRPE In Sg 1 Input HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000962 962 GSM945272 Stam UW DS16014 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHrpeInputStdRawRep1 None RawSignal retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpIC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeH3k4me3StdRawRep2 HRPE H3K4M3 Sg 2 H3K4me3 HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000961 961 GSM945271 Stam UW DS16188 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHrpeH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpIC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeH3k4me3StdRawRep1 HRPE H3K4M3 Sg 1 H3K4me3 HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000961 961 GSM945271 Stam UW DS16189 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHrpeH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRPEpIC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreInputStdRawRep1 HRE In Sg 1 Input HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000467 467 GSM945257 Stam UW DS11549 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHreInputStdRawRep1 None RawSignal renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k36me3StdRawRep2 HRE H3K36M3 Sg 2 H3K36me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000430 430 GSM945232 Stam UW DS12418 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHreH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k36me3StdRawRep1 HRE H3K36M3 Sg 1 H3K36me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000430 430 GSM945232 Stam UW DS12234 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHreH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k27me3StdRawRep2 HRE H3K27M3 Sg 2 H3K27me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000429 429 GSM945160 Stam UW DS12415 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHreH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k27me3StdRawRep1 HRE H3K27M3 Sg 1 H3K27me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000429 429 GSM945160 Stam UW DS12422 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHreH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k4me3StdRawRep2 HRE H3K4M3 Sg 2 H3K4me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-13 2010-07-12 wgEncodeEH000409 409 GSM945276 Stam UW DS11573 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHreH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k4me3StdRawRep1 HRE H3K4M3 Sg 1 H3K4me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000409 409 GSM945276 Stam UW DS11575 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHreH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HRE H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfInputStdRawRep1 HPF In Sg 1 Input HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000960 960 GSM945270 Stam UW DS16180 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHpfInputStdRawRep1 None RawSignal pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfH3k4me3StdRawRep2 HPF H3K4M3 Sg 2 H3K4me3 HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000959 959 GSM945284 Stam UW DS16183 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHpfH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfH3k4me3StdRawRep1 HPF H3K4M3 Sg 1 H3K4me3 HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000959 959 GSM945284 Stam UW DS16184 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHpfH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafInputStdRawRep1 HPAF In Sg 1 Input HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000958 958 GSM945285 Stam UW DS16177 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHpafInputStdRawRep1 None RawSignal pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafH3k4me3StdRawRep2 HPAF H3K4M3 Sg 2 H3K4me3 HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000957 957 GSM945292 Stam UW DS16154 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHpafH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafH3k4me3StdRawRep1 HPAF H3K4M3 Sg 1 H3K4me3 HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000957 957 GSM945292 Stam UW DS16153 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHpafH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HPAF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfInputStdRawRep1 HMF In Sg 1 Input HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000956 956 GSM945293 Stam UW DS16174 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHmfInputStdRawRep1 None RawSignal mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfH3k4me3StdRawRep2 HMF H3K4M3 Sg 2 H3K4me3 HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000955 955 GSM945290 Stam UW DS16152 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHmfH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfH3k4me3StdRawRep1 HMF H3K4M3 Sg 1 H3K4me3 HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000955 955 GSM945290 Stam UW DS16151 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHmfH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecInputStdRawRep1 HMEC In Sg 1 Input HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000466 466 GSM945258 Stam UW DS13600 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHmecInputStdRawRep1 None RawSignal mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k27me3StdRawRep1 HMEC H3K27M3 Sg 1 H3K27me3 HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000408 408 GSM945277 Stam UW DS12082 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHmecH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k4me3StdRawRep2 HMEC H3K4M3 Sg 2 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000954 954 GSM945159 Stam UW DS15761 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHmecH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k4me3StdRawRep1 HMEC H3K4M3 Sg 1 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000954 954 GSM945159 Stam UW DS15762 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHmecH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HMEC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60InputStdRawRep1 HL-60 In Sg 1 Input HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000465 465 GSM945255 Stam UW DS13664 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHl60InputStdRawRep1 None RawSignal promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60H3k4me3StdRawRep2 HL-60 H3K4M3 Sg 2 H3K4me3 HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000418 418 GSM945222 Stam UW DS11797 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHl60H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60H3k4me3StdRawRep1 HL-60 H3K4M3 Sg 1 H3K4me3 HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000418 418 GSM945222 Stam UW DS11795 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHl60H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HL-60 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycInputStdRawRep1 HFMc In Sg 1 Input HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001896 1896 GSM945281 Stam UW DS18321 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHffmycInputStdRawRep1 None RawSignal foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFFMyc Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycH3k04me3StdRawRep2 HFMc H3K4M3 Sg 2 H3K4me3 HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001908 1908 GSM945239 Stam UW DS18325 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHffmycH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFFMyc H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycH3k04me3StdRawRep1 HFMc H3K4M3 Sg 1 H3K4me3 HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001908 1908 GSM945239 Stam UW DS18324 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHffmycH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFFMyc H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffInputStdRawRep1 HFF In Sg 1 Input HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002043 2043 GSM945219 Stam UW DS18316 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHffInputStdRawRep1 None RawSignal foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffH3k04me3StdRawRep1 HFF H3K4M3 Sg 1 H3K4me3 HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002042 2042 GSM945218 Stam UW DS18320 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHffH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HFF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293InputStdRawRep1 HEK In Sg 1 Input HEK293 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000464 464 GSM945256 Stam UW DS13603 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHek293InputStdRawRep1 None RawSignal embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEK293 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293H3k4me3StdRawRep2 HEK H3K4M3 Sg 2 H3K4me3 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000953 953 GSM945288 Stam UW DS15759 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHek293H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEK293 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293H3k4me3StdRawRep1 HEK H3K4M3 Sg 1 H3K4me3 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000953 953 GSM945288 Stam UW DS15760 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHek293H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEK293 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeInputStdRawRep1 HEE In Sg 1 Input HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000952 952 GSM945289 Stam UW DS16057 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHeeInputStdRawRep1 None RawSignal esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpIC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeH3k4me3StdRawRep2 HEE H3K4M3 Sg 2 H3K4me3 HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000951 951 GSM945286 Stam UW DS16061 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHeeH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpIC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeH3k4me3StdRawRep1 HEE H3K4M3 Sg 1 H3K4me3 HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000951 951 GSM945286 Stam UW DS16060 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHeeH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HEEpIC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116InputStdRawRep1 HCT16 In Sg 1 Input HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000950 950 GSM945287 Stam UW DS16013 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHct116InputStdRawRep1 None RawSignal colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116H3k4me3StdRawRep2 HCT16 H3K4M3 Sg 2 H3K4me3 HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000949 949 GSM945304 Stam UW DS16055 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHct116H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116H3k4me3StdRawRep1 HCT16 H3K4M3 Sg 1 H3K4me3 HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000949 949 GSM945304 Stam UW DS16056 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHct116H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCT-116 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeInputStdRawRep1 HCPE In Sg 1 Input HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000948 948 GSM945303 Stam UW DS15917 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHcpeInputStdRawRep1 None RawSignal choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpiC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeH3k4me3StdRawRep2 HCPE H3K4M3 Sg 2 H3K4me3 HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000947 947 GSM945306 Stam UW DS15757 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHcpeH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpiC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeH3k4me3StdRawRep1 HCPE H3K4M3 Sg 1 H3K4me3 HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000947 947 GSM945306 Stam UW DS15758 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHcpeH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCPEpiC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmInputStdRawRep1 HCM In Sg 1 Input HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000946 946 GSM945305 Stam UW DS15916 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHcmInputStdRawRep1 None RawSignal cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmH3k4me3StdRawRep2 HCM H3K4M3 Sg 2 H3K4me3 HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000945 945 GSM945308 Stam UW DS15756 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHcmH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmH3k4me3StdRawRep1 HCM H3K4M3 Sg 1 H3K4me3 HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000945 945 GSM945308 Stam UW DS15755 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHcmH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCM H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfaaInputStdRawRep1 HCFa In Sg 1 Input HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000944 944 GSM945307 Stam UW DS15915 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHcfaaInputStdRawRep1 None RawSignal cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCFaa Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfaaH3k4me3StdRawRep1 HCFa H3K4M3 Sg 1 H3K4me3 HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000943 943 GSM945310 Stam UW DS15754 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHcfaaH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCFaa H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfInputStdRawRep1 HCF In Sg 1 Input HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000942 942 GSM945309 Stam UW DS15914 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHcfInputStdRawRep1 None RawSignal cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfH3k4me3StdRawRep2 HCF H3K4M3 Sg 2 H3K4me3 HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000941 941 GSM945312 Stam UW DS15753 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHcfH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfH3k4me3StdRawRep1 HCF H3K4M3 Sg 1 H3K4me3 HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000941 941 GSM945312 Stam UW DS15751 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHcfH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HCF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecInputStdRawRep1 HBMEC In Sg 1 Input HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000940 940 GSM945311 Stam UW DS15913 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHbmecInputStdRawRep1 None RawSignal brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecH3k4me3StdRawRep2 HBMEC H3K4M3 Sg 2 H3K4me3 HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000939 939 GSM945163 Stam UW DS15748 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHbmecH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecH3k4me3StdRawRep1 HBMEC H3K4M3 Sg 1 H3K4me3 HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000939 939 GSM945163 Stam UW DS15749 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHbmecH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HBMEC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspInputStdRawRep1 HAsp In Sg 1 Input HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000974 974 GSM945248 Stam UW DS16041 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHaspInputStdRawRep1 None RawSignal astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspH3k4me3StdRawRep2 HAsp H3K4M3 Sg 2 H3K4me3 HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000973 973 GSM945249 Stam UW DS16045 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHaspH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspH3k4me3StdRawRep1 HAsp H3K4M3 Sg 1 H3K4me3 HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000973 973 GSM945249 Stam UW DS16044 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHaspH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HA-sp H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacInputStdRawRep1 HAc In Sg 1 Input HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-07-28 2012-04-28 wgEncodeEH002165 2165 GSM945227 Stam UW DS18311 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneHacInputStdRawRep1 None RawSignal astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacH3k04me3StdRawRep2 HAc H3K4M3 Sg 2 H3K4me3 HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001907 1907 GSM945242 Stam UW DS18314 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHacH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacH3k04me3StdRawRep1 HAc H3K4M3 Sg 1 H3K4me3 HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001907 1907 GSM945242 Stam UW DS18315 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneHacH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HAc H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esInputStdRawRep1 H7ES In Sg 1 Input H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000926 926 GSM945186 Stam UW DS14109 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneH7esInputStdRawRep1 None RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esInputStdDiffa14dRawRep1 H7ES In Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002532 2532 GSM945319 Stam UW DS14111 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneH7esInputStdDiffa14dRawRep1 diffProtA_14d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC Input diffProtA 14 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esInputStdDiffa9dRawRep1 H7ES In Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002545 2545 GSM945193 Stam UW DS15393 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneH7esInputStdDiffa9dRawRep1 diffProtA_9d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC Input diffProtA 9 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esInputStdDiffa5dRawRep1 H7ES In Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002544 2544 GSM945194 Stam UW DS14110 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneH7esInputStdDiffa5dRawRep1 diffProtA_5d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC Input diffProtA 5 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esInputStdDiffa2dRawRep1 H7ES In Sg 1 Input H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002543 2543 GSM945189 Stam UW DS15392 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneH7esInputStdDiffa2dRawRep1 diffProtA_2d RawSignal undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC Input diffProtA 2 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdRawRep2 H7ES H3K36M3 Sg 2 H3K36me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000924 924 GSM945184 Stam UW DS14114 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdRawRep1 H7ES H3K36M3 Sg 1 H3K36me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000924 924 GSM945184 Stam UW DS14115 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa14dRawRep2 H7ES H3K36M3 Sg 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002537 2537 GSM945324 Stam UW DS14650 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa14dRawRep2 diffProtA_14d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 14 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa14dRawRep1 H7ES H3K36M3 Sg 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002537 2537 GSM945324 Stam UW DS14123 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa14dRawRep1 diffProtA_14d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 14 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa9dRawRep2 H7ES H3K36M3 Sg 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002540 2540 GSM945192 Stam UW DS15386 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa9dRawRep2 diffProtA_9d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 9 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa9dRawRep1 H7ES H3K36M3 Sg 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002540 2540 GSM945192 Stam UW DS14648 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa9dRawRep1 diffProtA_9d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 9 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa5dRawRep2 H7ES H3K36M3 Sg 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002539 2539 GSM945316 Stam UW DS14120 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa5dRawRep2 diffProtA_5d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 5 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa5dRawRep1 H7ES H3K36M3 Sg 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002539 2539 GSM945316 Stam UW DS14119 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa5dRawRep1 diffProtA_5d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 5 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa2dRawRep2 H7ES H3K36M3 Sg 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002538 2538 GSM945315 Stam UW DS14646 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa2dRawRep2 diffProtA_2d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 2 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa2dRawRep1 H7ES H3K36M3 Sg 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002538 2538 GSM945315 Stam UW DS15385 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa2dRawRep1 diffProtA_2d RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K36me3 diffProtA 2 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdRawRep2 H7ES H3K27M3 Sg 2 H3K27me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000923 923 GSM945183 Stam UW DS14113 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdRawRep1 H7ES H3K27M3 Sg 1 H3K27me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000923 923 GSM945183 Stam UW DS13428 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa14dRawRep2 H7ES H3K27M3 Sg 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002533 2533 GSM945320 Stam UW DS14122 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa14dRawRep2 diffProtA_14d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 14 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa14dRawRep1 H7ES H3K27M3 Sg 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002533 2533 GSM945320 Stam UW DS14649 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa14dRawRep1 diffProtA_14d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 14 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa9dRawRep2 H7ES H3K27M3 Sg 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002536 2536 GSM945323 Stam UW DS14709 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa9dRawRep2 diffProtA_9d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 9 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa9dRawRep1 H7ES H3K27M3 Sg 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002536 2536 GSM945323 Stam UW DS14647 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa9dRawRep1 diffProtA_9d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 9 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa5dRawRep2 H7ES H3K27M3 Sg 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002535 2535 GSM945326 Stam UW DS14118 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa5dRawRep2 diffProtA_5d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 5 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa5dRawRep1 H7ES H3K27M3 Sg 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002535 2535 GSM945326 Stam UW DS13778 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa5dRawRep1 diffProtA_5d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 5 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa2dRawRep2 H7ES H3K27M3 Sg 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002534 2534 GSM945325 Stam UW DS14708 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa2dRawRep2 diffProtA_2d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 2 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa2dRawRep1 H7ES H3K27M3 Sg 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002534 2534 GSM945325 Stam UW DS14645 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa2dRawRep1 diffProtA_2d RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K27me3 diffProtA 2 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k4me3StdRawRep2 H7ES H3K4M3 Sg 2 H3K4me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000925 925 GSM945185 Stam UW DS14112 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k4me3StdRawRep1 H7ES H3K4M3 Sg 1 H3K4me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000925 925 GSM945185 Stam UW DS13427 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa14dRawRep2 H7ES H3K4M3 Sg 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-04-04 2013-01-04 wgEncodeEH002530 2530 GSM945321 Stam UW DS14707 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa14dRawRep2 diffProtA_14d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 14 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa14dRawRep1 H7ES H3K4M3 Sg 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002530 2530 GSM945321 Stam UW DS14121 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa14dRawRep1 diffProtA_14d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 14 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa9dRawRep2 H7ES H3K4M3 Sg 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002542 2542 GSM945190 Stam UW DS14705 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa9dRawRep2 diffProtA_9d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 9 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa9dRawRep1 H7ES H3K4M3 Sg 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002542 2542 GSM945190 Stam UW DS14706 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa9dRawRep1 diffProtA_9d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 9 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa5dRawRep2 H7ES H3K4M3 Sg 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002531 2531 GSM945322 Stam UW DS14116 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa5dRawRep2 diffProtA_5d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 5 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa5dRawRep1 H7ES H3K4M3 Sg 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-04-04 2013-01-04 wgEncodeEH002531 2531 GSM945322 Stam UW DS13777 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa5dRawRep1 diffProtA_5d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 5 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa2dRawRep2 H7ES H3K4M3 Sg 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002541 2541 GSM945191 Stam UW DS14703 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa2dRawRep2 diffProtA_2d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 2 d Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa2dRawRep1 H7ES H3K4M3 Sg 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002541 2541 GSM945191 Stam UW DS14704 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa2dRawRep1 diffProtA_2d RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Shows the density of mapped reads on the plus and minus strands (wiggle format) H7-hESC H3K4me3 diffProtA 2 d Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12875InputStdRawRep1 GM75 In Sg 1 Input GM12875 std ChipSeq ENCODE Mar 2012 Freeze 2010-06-15 2010-11-18 wgEncodeEH000462 462 GSM945260 Stam UW DS13589 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneGm12875InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12875 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12875H3k04me3StdRawRep1 GM75 H3K4M3 Sg 1 H3K4me3 GM12875 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002041 2041 GSM945221 Stam UW DS18910 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneGm12875H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12875 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865InputStdRawRep1 GM65 In Sg 1 Input GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2010-06-15 2010-11-18 wgEncodeEH000458 458 GSM945234 Stam UW DS13590 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneGm12865InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865H3k04me3StdRawRep2 GM65 H3K4M3 Sg 2 H3K4me3 GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002039 2039 GSM945295 Stam UW DS20810 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneGm12865H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865H3k04me3StdRawRep1 GM65 H3K4M3 Sg 1 H3K4me3 GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002039 2039 GSM945295 Stam UW DS18707 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneGm12865H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12865 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864InputStdRawRep1 GM64 In Sg 1 Input GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2010-06-15 2010-11-18 wgEncodeEH000457 457 GSM945238 Stam UW DS13587 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneGm12864InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864H3k04me3StdRawRep2 GM64 H3K4M3 Sg 2 H3K4me3 GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002038 2038 GSM945296 Stam UW DS18900 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneGm12864H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864H3k04me3StdRawRep1 GM64 H3K4M3 Sg 1 H3K4me3 GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002038 2038 GSM945296 Stam UW DS18706 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneGm12864H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12864 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990InputStdRawRep1 GM90 In Sg 1 Input GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000455 455 GSM945237 Stam UW DS11497 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneGm06990InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k36me3StdRawRep2 GM90 H3K36M3 Sg 2 H3K36me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000444 444 GSM945213 Stam UW DS12189 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneGm06990H3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k36me3StdRawRep1 GM90 H3K36M3 Sg 1 H3K36me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000444 444 GSM945213 Stam UW DS12192 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneGm06990H3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k27me3StdRawRep2 GM90 H3K27M3 Sg 2 H3K27me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000427 427 GSM945205 Stam UW DS12188 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneGm06990H3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k27me3StdRawRep1 GM90 H3K27M3 Sg 1 H3K27me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000427 427 GSM945205 Stam UW DS12191 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneGm06990H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k4me3StdRawRep2 GM90 H3K4M3 Sg 2 H3K4me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-12 2010-07-11 wgEncodeEH000417 417 GSM945179 Stam UW DS11519 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneGm06990H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k4me3StdRawRep1 GM90 H3K4M3 Sg 1 H3K4me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-13 2010-07-12 wgEncodeEH000417 417 GSM945179 Stam UW DS11521 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneGm06990H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM06990 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2InputStdRawRep1 Caco In Sg 1 Input Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000454 454 GSM945236 Stam UW DS13597 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneCaco2InputStdRawRep1 None RawSignal colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k36me3StdRawRep2 Caco H3K36M3 Sg 2 H3K36me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000426 426 GSM945206 Stam UW DS12405 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneCaco2H3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k36me3StdRawRep1 Caco H3K36M3 Sg 1 H3K36me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000426 426 GSM945206 Stam UW DS12406 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneCaco2H3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k27me3StdRawRep2 Caco H3K27M3 Sg 2 H3K27me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000425 425 GSM945203 Stam UW DS12218 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneCaco2H3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k27me3StdRawRep1 Caco H3K27M3 Sg 1 H3K27me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-20 2010-07-20 wgEncodeEH000425 425 GSM945203 Stam UW DS12221 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneCaco2H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k4me3StdRawRep2 Caco H3K4M3 Sg 2 H3K4me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-09-29 2010-06-29 wgEncodeEH000407 407 GSM945162 Stam UW DS11785 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneCaco2H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k4me3StdRawRep1 Caco H3K4M3 Sg 1 H3K4me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-09-29 2010-06-29 wgEncodeEH000407 407 GSM945162 Stam UW DS11784 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneCaco2H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Caco-2 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjInputStdRawRep1 BJ In Sg 1 Input BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000453 453 GSM945235 Stam UW DS11544 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneBjInputStdRawRep1 None RawSignal skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k36me3StdRawRep2 BJ H3K36M3 Sg 2 H3K36me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000443 443 GSM945207 Stam UW DS12195 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneBjH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k36me3StdRawRep1 BJ H3K36M3 Sg 1 H3K36me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000443 443 GSM945207 Stam UW DS12198 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneBjH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k27me3StdRawRep2 BJ H3K27M3 Sg 2 H3K27me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-20 2010-07-20 wgEncodeEH000424 424 GSM945204 Stam UW DS12197 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneBjH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k27me3StdRawRep1 BJ H3K27M3 Sg 1 H3K27me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000424 424 GSM945204 Stam UW DS12194 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneBjH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k4me3StdRawRep2 BJ H3K4M3 Sg 2 H3K4me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-12 2010-07-11 wgEncodeEH000416 416 GSM945178 Stam UW DS11561 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneBjH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k4me3StdRawRep1 BJ H3K4M3 Sg 1 H3K4me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-13 2010-07-12 wgEncodeEH000416 416 GSM945178 Stam UW DS11563 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneBjH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BJ H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cInputStdRawRep1 BE2_C In Sg 1 Input BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001892 1892 GSM945283 Stam UW DS18306 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneBe2cInputStdRawRep1 None RawSignal neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2_C Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cH3k04me3StdRawRep2 BE2_C H3K4M3 Sg 2 H3K4me3 BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001906 1906 GSM945241 Stam UW DS18310 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneBe2cH3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2_C H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cH3k04me3StdRawRep1 BE2_C H3K4M3 Sg 1 H3K4me3 BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001906 1906 GSM945241 Stam UW DS18309 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneBe2cH3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) BE2_C H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafInputStdRawRep1 AoAF In Sg 1 Input AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000938 938 GSM945164 Stam UW DS15912 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneAoafInputStdRawRep1 None RawSignal aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafH3k4me3StdRawRep2 AoAF H3K4M3 Sg 2 H3K4me3 AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000937 937 GSM945170 Stam UW DS15747 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAoafH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafH3k4me3StdRawRep1 AoAF H3K4M3 Sg 1 H3K4me3 AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000937 937 GSM945170 Stam UW DS15746 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAoafH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AoAF H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803InputStdRawRep1 AG03 In Sg 1 Input AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000936 936 GSM945171 Stam UW DS15911 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneAg10803InputStdRawRep1 None RawSignal abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803H3k4me3StdRawRep2 AG03 H3K4M3 Sg 2 H3K4me3 AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000935 935 GSM945172 Stam UW DS15745 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAg10803H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803H3k4me3StdRawRep1 AG03 H3K4M3 Sg 1 H3K4me3 AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000935 935 GSM945172 Stam UW DS15744 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg10803H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG10803 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319InputStdRawRep1 AG19 In Sg 1 Input AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000934 934 GSM945173 Stam UW DS15910 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneAg09319InputStdRawRep1 None RawSignal gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319H3k4me3StdRawRep2 AG19 H3K4M3 Sg 2 H3K4me3 AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000933 933 GSM945166 Stam UW DS15743 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAg09319H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319H3k4me3StdRawRep1 AG19 H3K4M3 Sg 1 H3K4me3 AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000933 933 GSM945166 Stam UW DS15742 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg09319H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09319 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309InputStdRawRep1 AG09 In Sg 1 Input AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000932 932 GSM945167 Stam UW DS16030 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneAg09309InputStdRawRep1 None RawSignal adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309H3k4me3StdRawRep2 AG09 H3K4M3 Sg 2 H3K4me3 AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000931 931 GSM945168 Stam UW DS16033 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAg09309H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309H3k4me3StdRawRep1 AG09 H3K4M3 Sg 1 H3K4me3 AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000931 931 GSM945168 Stam UW DS16034 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg09309H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG09309 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450InputStdRawRep1 AG50 In Sg 1 Input AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000930 930 GSM945169 Stam UW DS15909 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneAg04450InputStdRawRep1 None RawSignal fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k27me3StdRawRep1 AG50 H3K27m3 Rw 1 H3K27me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003036 3036 GSM1010913 Stam UW DS21480 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg04450H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k27acStdRawRep1 AG50 H3K27ac Rw 1 H3K27ac AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003035 3035 GSM1010912 Stam UW DS21479 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg04450H3k27acStdRawRep1 None RawSignal Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 H3K27ac Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k09me3StdRawRep2 AG50 H3K9m3 Raw 2 H3K9me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003037 3037 GSM1010914 Stam UW DS21481 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAg04450H3k09me3StdRawRep2 None RawSignal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 H3K9me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k09me3StdRawRep1 AG50 H3K9m3 Raw 1 H3K9me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003037 3037 GSM1010914 Stam UW DS21482 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg04450H3k09me3StdRawRep1 None RawSignal Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 H3K9me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k4me3StdRawRep2 AG50 H3K4M3 Sg 2 H3K4me3 AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000929 929 GSM945177 Stam UW DS15741 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAg04450H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k4me3StdRawRep1 AG50 H3K4M3 Sg 1 H3K4me3 AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000929 929 GSM945177 Stam UW DS15740 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg04450H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04450 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449InputStdRawRep1 AG49 In Sg 1 Input AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000928 928 GSM945176 Stam UW DS15908 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneAg04449InputStdRawRep1 None RawSignal fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449H3k4me3StdRawRep2 AG49 H3K4M3 Sg 2 H3K4me3 AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000927 927 GSM945187 Stam UW DS15739 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneAg04449H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449H3k4me3StdRawRep1 AG49 H3K4M3 Sg 1 H3K4me3 AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000927 927 GSM945187 Stam UW DS15737 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneAg04449H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) AG04449 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746InputStdRawRep1 CD14 In Sg 1 Input Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002169 2169 GSM945224 Stam UW DS18980 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneMonocd14ro1746InputStdRawRep1 None RawSignal Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Monocytes-CD14+ RO 01746 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746H3k27me3StdRawRep1 CD14 H3K27M3 Sg 1 H3K27me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002167 2167 GSM945301 Stam UW DS19094 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneMonocd14ro1746H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Monocytes-CD14+ RO 01746 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746H3k04me3StdRawRep1 CD14 H3K4M3 Sg 1 H3K4me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002168 2168 GSM945225 Stam UW DS18981 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneMonocd14ro1746H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) Monocytes-CD14+ RO 01746 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7InputStdRawRep1 MCF7 In Sg 1 Input MCF-7 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000968 968 GSM945274 Stam UW DS16198 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneMcf7InputStdRawRep1 None RawSignal mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7H3k04me3StdRawRep2 MCF7 H3K4M3 Sg 2 H3K4me3 MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000967 967 GSM945269 Stam UW DS16201 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneMcf7H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7H3k4me3StdRawRep1 MCF7 H3K4M3 Sg 1 H3K4me3 MCF-7 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000967 967 GSM945269 Stam UW DS16202 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneMcf7H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) MCF-7 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecInputStdRawRep1 HUVE In Sg 1 Input HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000468 468 GSM945254 Stam UW DS11470 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHuvecInputStdRawRep1 None RawSignal umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k36me3StdRawRep2 HUVE H3K36M3 Sg 2 H3K36me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000431 431 GSM945233 Stam UW DS12225 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHuvecH3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k36me3StdRawRep1 HUVE H3K36M3 Sg 1 H3K36me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000431 431 GSM945233 Stam UW DS12228 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHuvecH3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k27me3StdRawRep2 HUVE H3K27M3 Sg 2 H3K27me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-12 wgEncodeEH000411 411 GSM945180 Stam UW DS12224 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHuvecH3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k27me3StdRawRep1 HUVE H3K27M3 Sg 1 H3K27me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000411 411 GSM945180 Stam UW DS12227 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHuvecH3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k4me3StdRawRep2 HUVE H3K4M3 Sg 2 H3K4me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-13 2010-07-12 wgEncodeEH000412 412 GSM945181 Stam UW DS11458 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHuvecH3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k4me3StdRawRep1 HUVE H3K4M3 Sg 1 H3K4me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000412 412 GSM945181 Stam UW DS11460 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHuvecH3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HUVEC H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2InputStdRawRep1 HepG In Sg 1 Input HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000470 470 GSM945291 Stam UW DS13599 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHepg2InputStdRawRep1 None RawSignal hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k36me3StdRawRep2 HepG H3K36M3 Sg 2 H3K36me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000446 446 GSM945211 Stam UW DS12075 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneHepg2H3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k36me3StdRawRep1 HepG H3K36M3 Sg 1 H3K36me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000446 446 GSM945211 Stam UW DS12207 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHepg2H3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k27me3StdRawRep2 HepG H3K27M3 Sg 2 H3K27me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000433 433 GSM945231 Stam UW DS12206 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHepg2H3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k27me3StdRawRep1 HepG H3K27M3 Sg 1 H3K27me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000433 433 GSM945231 Stam UW DS12076 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHepg2H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k4me3StdRawRep2 HepG H3K4M3 Sg 2 H3K4me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-09-29 2010-06-29 wgEncodeEH000413 413 GSM945182 Stam UW DS11780 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHepg2H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k4me3StdRawRep1 HepG H3K4M3 Sg 1 H3K4me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-09-29 2010-06-29 wgEncodeEH000413 413 GSM945182 Stam UW DS11781 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHepg2H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HepG2 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3InputStdRawRep1 HeLa In Sg 1 Input HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000469 469 GSM945253 Stam UW DS11540 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneHelas3InputStdRawRep1 None RawSignal cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k36me3StdRawRep2 HeLa H3K36M3 Sg 2 H3K36me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000432 432 GSM945230 Stam UW DS12201 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHelas3H3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k36me3StdRawRep1 HeLa H3K36M3 Sg 1 H3K36me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000432 432 GSM945230 Stam UW DS12071 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHelas3H3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k27me3StdRawRep2 HeLa H3K27M3 Sg 2 H3K27me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000442 442 GSM945208 Stam UW DS12070 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHelas3H3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k27me3StdRawRep1 HeLa H3K27M3 Sg 1 H3K27me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000442 442 GSM945208 Stam UW DS12072 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHelas3H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k4me3StdRawRep2 HeLa H3K4M3 Sg 2 H3K4me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-13 2010-07-12 wgEncodeEH000423 423 GSM945201 Stam UW DS11553 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneHelas3H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k4me3StdRawRep1 HeLa H3K4M3 Sg 1 H3K4me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-13 2010-07-12 wgEncodeEH000423 423 GSM945201 Stam UW DS11555 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneHelas3H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) HeLa-S3 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01794InputStdRawRep1 20+94 In Sg 1 Input CD20+_RO01794 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEH002172 2172 GSM945195 Stam UW DS18982 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneCd20ro01794InputStdRawRep1 None RawSignal B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ (RO 01794) Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01794H3k04me3StdRawRep3 20+94 H3K4M3 Sg 3 H3K4me3 CD20+_RO01794 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEH002171 2171 GSM945198 Stam UW DS18983 WindowDensity-bin20-win+/-75 hg19 3 exp wgEncodeUwHistoneCd20ro01794H3k04me3StdRawRep3 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ (RO 01794) H3K4me3 Histone Mod ChIP-seq Raw Sig 3 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778InputStdRawRep1 20+78 In Sg 1 Input CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-25 wgEncodeEH002170 2170 GSM945197 Stam UW DS18984 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneCd20ro01778InputStdRawRep1 None RawSignal B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ (RO 01778) Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778H3k04me3StdRawRep2 20+78 H3K4M3 Sg 2 H3K4me3 CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002166 2166 GSM945229 Stam UW DS18986 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneCd20ro01778H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ (RO 01778) H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778H3k04me3StdRawRep1 20+78 H3K4M3 Sg 1 H3K4me3 CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-14 2012-06-14 wgEncodeEH002166 2166 GSM945229 Stam UW DS18985 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneCd20ro01778H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) CD20+ (RO 01778) H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549InputStdRawRep1 A549 In Sg 1 Input A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEH001904 1904 GSM945243 Stam UW DS18301 WindowDensity-bin20-win+/-75 hg19 1 input wgEncodeUwHistoneA549InputStdRawRep1 None RawSignal epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549H3k04me3StdRawRep2 A549 H3K4M3 Sg 2 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001905 1905 GSM945244 Stam UW DS18304 WindowDensity-bin20-win+/-75 hg19 2 exp wgEncodeUwHistoneA549H3k04me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549H3k04me3StdRawRep1 A549 H3K4M3 Sg 1 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001905 1905 GSM945244 Stam UW DS18305 WindowDensity-bin20-win+/-75 hg19 1 exp wgEncodeUwHistoneA549H3k04me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) A549 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562InputStdRawRep1 K562 In Sg 1 Input K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000471 471 GSM945294 Stam UW DS11488 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneK562InputStdRawRep1 None RawSignal leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k36me3StdRawRep2 K562 H3K36M3 Sg 2 H3K36me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000435 435 GSM945302 Stam UW DS12177 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneK562H3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k36me3StdRawRep1 K562 H3K36M3 Sg 1 H3K36me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000435 435 GSM945302 Stam UW DS12067 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneK562H3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k27me3StdRawRep2 K562 H3K27M3 Sg 2 H3K27me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000434 434 GSM945228 Stam UW DS12068 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneK562H3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k27me3StdRawRep1 K562 H3K27M3 Sg 1 H3K27me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000434 434 GSM945228 Stam UW DS12066 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneK562H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k4me3StdRawRep2 K562 H3K4M3 Sg 2 H3K4me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000400 400 GSM945165 Stam UW DS11509 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneK562H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k4me3StdRawRep1 K562 H3K4M3 Sg 1 H3K4me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000400 400 GSM945165 Stam UW DS11507 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneK562H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) K562 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878InputStdRawRep1 GM78 In Sg 1 Input GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000463 463 GSM945259 Stam UW DS11883 WindowDensity-bin20-win+/-75 hg18 1 input wgEncodeUwHistoneGm12878InputStdRawRep1 None RawSignal B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 Input Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k36me3StdRawRep2 GM78 H3K36M3 Sg 2 H3K36me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000445 445 GSM945212 Stam UW DS12183 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneGm12878H3k36me3StdRawRep2 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 H3K36me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k36me3StdRawRep1 GM78 H3K36M3 Sg 1 H3K36me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000445 445 GSM945212 Stam UW DS12186 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneGm12878H3k36me3StdRawRep1 None RawSignal Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 H3K36me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k27me3StdRawRep2 GM78 H3K27M3 Sg 2 H3K27me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000428 428 GSM945196 Stam UW DS12185 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneGm12878H3k27me3StdRawRep2 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 H3K27me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k27me3StdRawRep1 GM78 H3K27M3 Sg 1 H3K27me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000428 428 GSM945196 Stam UW DS12182 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneGm12878H3k27me3StdRawRep1 None RawSignal Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 H3K27me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k4me3StdRawRep2 GM78 H3K4M3 Sg 2 H3K4me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-12 2010-07-11 wgEncodeEH000395 395 GSM945188 Stam UW DS11511 WindowDensity-bin20-win+/-75 hg18 2 exp wgEncodeUwHistoneGm12878H3k4me3StdRawRep2 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 H3K4me3 Histone Mod ChIP-seq Raw Sig 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k4me3StdRawRep1 GM78 H3K4M3 Sg 1 H3K4me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-06-30 2010-03-29 wgEncodeEH000395 395 GSM945188 Stam UW DS11513 WindowDensity-bin20-win+/-75 hg18 1 exp wgEncodeUwHistoneGm12878H3k4me3StdRawRep1 None RawSignal Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Shows the density of mapped reads on the plus and minus strands (wiggle format) GM12878 H3K4me3 Histone Mod ChIP-seq Raw Sig 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneViewPeaks Peaks Histone Modifications by ChIP-seq from ENCODE/University of Washington Regulation 
wgEncodeUwHistoneWi38H3k04me3StdPkRep2 WI38 H3K4M3 Pk 2 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001914 1914 GSM945265 Stam UW DS18349 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneWi38H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WI-38 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3StdPkRep1 WI38 H3K4M3 Pk 1 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001914 1914 GSM945265 Stam UW DS18350 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneWi38H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WI-38 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3OhtamStdPkRep2 WI38 H3K4M3 Pk 2 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002047 2047 GSM945215 Stam UW DS18354 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneWi38H3k04me3OhtamStdPkRep2 4OHTAM_20nM_72hr Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Regions of enriched signal in experiment WI-38 H3K4me3 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3OhtamStdPkRep1 WI38 H3K4M3 Pk 1 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002047 2047 GSM945215 Stam UW DS18355 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneWi38H3k04me3OhtamStdPkRep1 4OHTAM_20nM_72hr Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) Regions of enriched signal in experiment WI-38 H3K4me3 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1H3k04me3StdPkRep2 WERI H3K4M3 Pk 2 H3K4me3 WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001913 1913 GSM945263 Stam UW DS16213 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneWerirb1H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WERI-Rb-1 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1H3k04me3StdPkRep1 WERI H3K4M3 Pk 1 H3K4me3 WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001913 1913 GSM945263 Stam UW DS16214 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneWerirb1H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment WERI-Rb-1 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k36me3StdPkRep2 SKRA H3K36M3 Pk 2 H3K36me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000441 441 GSM945209 Stam UW DS12403 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneSknshraH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k36me3StdPkRep1 SKRA H3K36M3 Pk 1 H3K36me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000441 441 GSM945209 Stam UW DS12404 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneSknshraH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k27me3StdPkRep2 SKRA H3K27M3 Pk 2 H3K27me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000440 440 GSM945210 Stam UW DS12215 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneSknshraH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k27me3StdPkRep1 SKRA H3K27M3 Pk 1 H3K27me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000440 440 GSM945210 Stam UW DS12212 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneSknshraH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k4me3StdPkRep2 SKRA H3K4M3 Pk 2 H3K4me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000422 422 GSM945202 Stam UW DS11783 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneSknshraH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k4me3StdPkRep1 SKRA H3K4M3 Pk 1 H3K4me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000422 422 GSM945202 Stam UW DS11782 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneSknshraH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-SH_RA H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcH3k04me3StdPkRep2 SKNMC H3K4M3 Pk 2 H3K4me3 SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001912 1912 GSM945264 Stam UW DS18345 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneSknmcH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-MC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcH3k04me3StdPkRep1 SKNMC H3K4M3 Pk 1 H3K4me3 SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001912 1912 GSM945264 Stam UW DS18344 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneSknmcH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SK-N-MC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcH3k04me3StdPkRep2 SKMC H3K4M3 Pk 2 H3K4me3 SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002046 2046 GSM945214 Stam UW DS16212 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneSkmcH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SKMC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcH3k04me3StdPkRep1 SKMC H3K4M3 Pk 1 H3K4me3 SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002046 2046 GSM945214 Stam UW DS16211 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneSkmcH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SKMC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k36me3StdPkRep2 SAEC H3K36M3 Pk 2 H3K36me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000438 438 GSM945226 Stam UW DS12246 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneSaecH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k36me3StdPkRep1 SAEC H3K36M3 Pk 1 H3K36me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000438 438 GSM945226 Stam UW DS12243 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneSaecH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k27me3StdPkRep2 SAEC H3K27M3 Pk 2 H3K27me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000420 420 GSM945200 Stam UW DS12245 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneSaecH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k27me3StdPkRep1 SAEC H3K27M3 Pk 1 H3K27me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000420 420 GSM945200 Stam UW DS12242 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneSaecH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k4me3StdPkRep2 SAEC H3K4M3 Pk 2 H3K4me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000421 421 GSM945199 Stam UW DS11579 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneSaecH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k4me3StdPkRep1 SAEC H3K4M3 Pk 1 H3K4me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000421 421 GSM945199 Stam UW DS11577 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneSaecH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment SAEC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecH3k04me3StdPkRep2 RPTEC H3K4M3 Pk 2 H3K4me3 RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002044 2044 GSM945216 Stam UW DS18339 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneRptecH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPTEC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecH3k04me3StdPkRep1 RPTEC H3K4M3 Pk 1 H3K4me3 RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002044 2044 GSM945216 Stam UW DS18340 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneRptecH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment RPTEC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1H3k04me3StdPkRep2 PANC1 H3K4M3 Pk 2 H3K4me3 PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001911 1911 GSM945261 Stam UW DS18334 lmax-v1.0 hg19 2 exp wgEncodeUwHistonePanc1H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment PANC-1 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1H3k04me3StdPkRep1 PANC1 H3K4M3 Pk 1 H3K4me3 PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001911 1911 GSM945261 Stam UW DS18335 lmax-v1.0 hg19 1 exp wgEncodeUwHistonePanc1H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment PANC-1 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfH3k04me3StdPkRep2 NHLF H3K4M3 Pk 2 H3K4me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001910 1910 GSM945262 Stam UW DS16350 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneNhlfH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHLF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfH3k04me3StdPkRep1 NHLF H3K4M3 Pk 1 H3K4me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001910 1910 GSM945262 Stam UW DS16351 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneNhlfH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHLF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k36me3StdPkRep2 NHEK H3K36M3 Pk 2 H3K36me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000414 414 GSM945174 Stam UW DS12240 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneNhekH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k36me3StdPkRep1 NHEK H3K36M3 Pk 1 H3K36me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000414 414 GSM945174 Stam UW DS12237 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneNhekH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k27me3StdPkRep2 NHEK H3K27M3 Pk 2 H3K27me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-16 2011-03-15 wgEncodeEH000436 436 GSM945300 Stam UW DS12080 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneNhekH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k27me3StdPkRep1 NHEK H3K27M3 Pk 1 H3K27me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000436 436 GSM945300 Stam UW DS12078 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneNhekH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k4me3StdPkRep2 NHEK H3K4M3 Pk 2 H3K4me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000415 415 GSM945175 Stam UW DS11557 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneNhekH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k4me3StdPkRep1 NHEK H3K4M3 Pk 1 H3K4me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000415 415 GSM945175 Stam UW DS11559 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneNhekH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHEK H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoH3k4me3StdPkRep2 NHDF H3K4M3 Pk 2 H3K4me3 NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000971 971 GSM945251 Stam UW DS16207 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneNhdfneoH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-neo H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoH3k4me3StdPkRep1 NHDF H3K4M3 Pk 1 H3K4me3 NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000971 971 GSM945251 Stam UW DS16206 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneNhdfneoH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NHDF-neo H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNb4H3k4me3StdPkRep1 NB4 H3K4M3 Pk 1 H3K4me3 NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000969 969 GSM945275 Stam UW DS16346 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneNb4H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment NB4 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapH3k04me3StdPkRep2 LNCP H3K4M3 Pk 2 H3K4me3 LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001909 1909 GSM945240 Stam UW DS18329 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneLncapH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment LNCaP H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapH3k04me3StdPkRep1 LNCP H3K4M3 Pk 1 H3K4me3 LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001909 1909 GSM945240 Stam UW DS18330 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneLncapH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment LNCaP H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatH3k4me3StdPkRep2 Jurk H3K4M3 Pk 2 H3K4me3 Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000965 965 GSM945267 Stam UW DS16196 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneJurkatH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Jurkat H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatH3k4me3StdPkRep1 Jurk H3K4M3 Pk 1 H3K4me3 Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000965 965 GSM945267 Stam UW DS16197 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneJurkatH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Jurkat H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfH3k4me3StdPkRep2 HVMF H3K4M3 Pk 2 H3K4me3 HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000963 963 GSM945273 Stam UW DS16155 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHvmfH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HVMF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfH3k4me3StdPkRep1 HVMF H3K4M3 Pk 1 H3K4me3 HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000963 963 GSM945273 Stam UW DS16156 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHvmfH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HVMF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeH3k4me3StdPkRep2 HRPE H3K4M3 Pk 2 H3K4me3 HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000961 961 GSM945271 Stam UW DS16188 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHrpeH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRPEpIC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeH3k4me3StdPkRep1 HRPE H3K4M3 Pk 1 H3K4me3 HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000961 961 GSM945271 Stam UW DS16189 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHrpeH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRPEpIC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k36me3StdPkRep2 HRE H3K36M3 Pk 2 H3K36me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000430 430 GSM945232 Stam UW DS12418 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHreH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k36me3StdPkRep1 HRE H3K36M3 Pk 1 H3K36me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000430 430 GSM945232 Stam UW DS12234 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHreH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k27me3StdPkRep2 HRE H3K27M3 Pk 2 H3K27me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000429 429 GSM945160 Stam UW DS12415 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHreH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k27me3StdPkRep1 HRE H3K27M3 Pk 1 H3K27me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-20 2010-07-20 wgEncodeEH000429 429 GSM945160 Stam UW DS12422 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHreH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k4me3StdPkRep2 HRE H3K4M3 Pk 2 H3K4me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000409 409 GSM945276 Stam UW DS11573 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHreH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k4me3StdPkRep1 HRE H3K4M3 Pk 1 H3K4me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000409 409 GSM945276 Stam UW DS11575 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHreH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HRE H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfH3k4me3StdPkRep2 HPF H3K4M3 Pk 2 H3K4me3 HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000959 959 GSM945284 Stam UW DS16183 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHpfH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfH3k4me3StdPkRep1 HPF H3K4M3 Pk 1 H3K4me3 HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000959 959 GSM945284 Stam UW DS16184 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHpfH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafH3k4me3StdPkRep2 HPAF H3K4M3 Pk 2 H3K4me3 HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000957 957 GSM945292 Stam UW DS16154 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHpafH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafH3k4me3StdPkRep1 HPAF H3K4M3 Pk 1 H3K4me3 HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000957 957 GSM945292 Stam UW DS16153 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHpafH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HPAF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfH3k4me3StdPkRep2 HMF H3K4M3 Pk 2 H3K4me3 HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000955 955 GSM945290 Stam UW DS16152 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHmfH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfH3k4me3StdPkRep1 HMF H3K4M3 Pk 1 H3K4me3 HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000955 955 GSM945290 Stam UW DS16151 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHmfH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k27me3StdPkRep1 HMEC H3K27M3 Pk 1 H3K27me3 HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000408 408 GSM945277 Stam UW DS12082 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHmecH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k4me3StdPkRep2 HMEC H3K4M3 Pk 2 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000954 954 GSM945159 Stam UW DS15761 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHmecH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k4me3StdPkRep1 HMEC H3K4M3 Pk 1 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000954 954 GSM945159 Stam UW DS15762 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHmecH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HMEC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60H3k4me3StdPkRep2 HL-60 H3K4M3 Pk 2 H3K4me3 HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000418 418 GSM945222 Stam UW DS11797 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHl60H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HL-60 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60H3k4me3StdPkRep1 HL-60 H3K4M3 Pk 1 H3K4me3 HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000418 418 GSM945222 Stam UW DS11795 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHl60H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HL-60 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycH3k04me3StdPkRep2 HFMc H3K4M3 Pk 2 H3K4me3 HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001908 1908 GSM945239 Stam UW DS18325 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHffmycH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFFMyc H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycH3k04me3StdPkRep1 HFMc H3K4M3 Pk 1 H3K4me3 HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001908 1908 GSM945239 Stam UW DS18324 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHffmycH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFFMyc H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffH3k04me3StdPkRep1 HFF H3K4M3 Pk 1 H3K4me3 HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002042 2042 GSM945218 Stam UW DS18320 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHffH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HFF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293H3k4me3StdPkRep2 HEK H3K4M3 Pk 2 H3K4me3 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000953 953 GSM945288 Stam UW DS15759 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHek293H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEK293 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293H3k4me3StdPkRep1 HEK H3K4M3 Pk 1 H3K4me3 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000953 953 GSM945288 Stam UW DS15760 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHek293H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEK293 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeH3k4me3StdPkRep2 HEE H3K4M3 Pk 2 H3K4me3 HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000951 951 GSM945286 Stam UW DS16061 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHeeH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEEpIC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeH3k4me3StdPkRep1 HEE H3K4M3 Pk 1 H3K4me3 HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000951 951 GSM945286 Stam UW DS16060 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHeeH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HEEpIC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116H3k4me3StdPkRep2 HCT16 H3K4M3 Pk 2 H3K4me3 HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000949 949 GSM945304 Stam UW DS16055 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHct116H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCT-116 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116H3k4me3StdPkRep1 HCT16 H3K4M3 Pk 1 H3K4me3 HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000949 949 GSM945304 Stam UW DS16056 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHct116H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCT-116 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeH3k4me3StdPkRep2 HCPE H3K4M3 Pk 2 H3K4me3 HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000947 947 GSM945306 Stam UW DS15757 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHcpeH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpiC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeH3k4me3StdPkRep1 HCPE H3K4M3 Pk 1 H3K4me3 HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000947 947 GSM945306 Stam UW DS15758 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHcpeH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCPEpiC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmH3k4me3StdPkRep2 HCM H3K4M3 Pk 2 H3K4me3 HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000945 945 GSM945308 Stam UW DS15756 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHcmH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCM H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmH3k4me3StdPkRep1 HCM H3K4M3 Pk 1 H3K4me3 HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000945 945 GSM945308 Stam UW DS15755 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHcmH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCM H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfaaH3k4me3StdPkRep1 HCFa H3K4M3 Pk 1 H3K4me3 HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000943 943 GSM945310 Stam UW DS15754 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHcfaaH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCFaa H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfH3k4me3StdPkRep2 HCF H3K4M3 Pk 2 H3K4me3 HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000941 941 GSM945312 Stam UW DS15753 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHcfH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfH3k4me3StdPkRep1 HCF H3K4M3 Pk 1 H3K4me3 HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000941 941 GSM945312 Stam UW DS15751 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHcfH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HCF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecH3k4me3StdPkRep2 HBMEC H3K4M3 Pk 2 H3K4me3 HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000939 939 GSM945163 Stam UW DS15748 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHbmecH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBMEC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecH3k4me3StdPkRep1 HBMEC H3K4M3 Pk 1 H3K4me3 HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000939 939 GSM945163 Stam UW DS15749 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHbmecH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HBMEC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspH3k4me3StdPkRep2 HAsp H3K4M3 Pk 2 H3K4me3 HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000973 973 GSM945249 Stam UW DS16045 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHaspH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-sp H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspH3k4me3StdPkRep1 HAsp H3K4M3 Pk 1 H3K4me3 HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000973 973 GSM945249 Stam UW DS16044 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHaspH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HA-sp H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacH3k04me3StdPkRep2 HAc H3K4M3 Pk 2 H3K4me3 HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001907 1907 GSM945242 Stam UW DS18314 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneHacH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAc H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacH3k04me3StdPkRep1 HAc H3K4M3 Pk 1 H3K4me3 HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001907 1907 GSM945242 Stam UW DS18315 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneHacH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HAc H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdPkRep2 H7ES H3K36M3 Pk 2 H3K36me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000924 924 GSM945184 Stam UW DS14114 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdPkRep1 H7ES H3K36M3 Pk 1 H3K36me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000924 924 GSM945184 Stam UW DS14115 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa14dPkRep2 H7ES H3K36M3 Pk 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002537 2537 GSM945324 Stam UW DS14650 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa14dPkRep2 diffProtA_14d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 14 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa14dPkRep1 H7ES H3K36M3 Pk 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002537 2537 GSM945324 Stam UW DS14123 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa14dPkRep1 diffProtA_14d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 14 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa9dPkRep2 H7ES H3K36M3 Pk 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002540 2540 GSM945192 Stam UW DS15386 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa9dPkRep2 diffProtA_9d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 9 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa9dPkRep1 H7ES H3K36M3 Pk 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002540 2540 GSM945192 Stam UW DS14648 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa9dPkRep1 diffProtA_9d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 9 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa5dPkRep2 H7ES H3K36M3 Pk 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002539 2539 GSM945316 Stam UW DS14120 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa5dPkRep2 diffProtA_5d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 5 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa5dPkRep1 H7ES H3K36M3 Pk 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002539 2539 GSM945316 Stam UW DS14119 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa5dPkRep1 diffProtA_5d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 5 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa2dPkRep2 H7ES H3K36M3 Pk 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002538 2538 GSM945315 Stam UW DS14646 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa2dPkRep2 diffProtA_2d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 2 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa2dPkRep1 H7ES H3K36M3 Pk 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002538 2538 GSM945315 Stam UW DS15385 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa2dPkRep1 diffProtA_2d Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K36me3 diffProtA 2 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdPkRep2 H7ES H3K27M3 Pk 2 H3K27me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000923 923 GSM945183 Stam UW DS14113 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdPkRep1 H7ES H3K27M3 Pk 1 H3K27me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000923 923 GSM945183 Stam UW DS13428 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa14dPkRep2 H7ES H3K27M3 Pk 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002533 2533 GSM945320 Stam UW DS14122 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa14dPkRep2 diffProtA_14d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 14 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa14dPkRep1 H7ES H3K27M3 Pk 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002533 2533 GSM945320 Stam UW DS14649 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa14dPkRep1 diffProtA_14d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 14 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa9dPkRep2 H7ES H3K27M3 Pk 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002536 2536 GSM945323 Stam UW DS14709 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa9dPkRep2 diffProtA_9d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 9 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa9dPkRep1 H7ES H3K27M3 Pk 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002536 2536 GSM945323 Stam UW DS14647 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa9dPkRep1 diffProtA_9d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 9 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa5dPkRep2 H7ES H3K27M3 Pk 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002535 2535 GSM945326 Stam UW DS14118 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa5dPkRep2 diffProtA_5d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 5 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa5dPkRep1 H7ES H3K27M3 Pk 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002535 2535 GSM945326 Stam UW DS13778 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa5dPkRep1 diffProtA_5d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 5 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa2dPkRep2 H7ES H3K27M3 Pk 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002534 2534 GSM945325 Stam UW DS14708 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa2dPkRep2 diffProtA_2d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 2 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa2dPkRep1 H7ES H3K27M3 Pk 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002534 2534 GSM945325 Stam UW DS14645 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa2dPkRep1 diffProtA_2d Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K27me3 diffProtA 2 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k4me3StdPkRep2 H7ES H3K4M3 Pk 2 H3K4me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000925 925 GSM945185 Stam UW DS14112 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k4me3StdPkRep1 H7ES H3K4M3 Pk 1 H3K4me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000925 925 GSM945185 Stam UW DS13427 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment H7-hESC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa14dPkRep2 H7ES H3K4M3 Pk 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-04-04 2013-01-04 wgEncodeEH002530 2530 GSM945321 Stam UW DS14707 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa14dPkRep2 diffProtA_14d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 14 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa14dPkRep1 H7ES H3K4M3 Pk 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002530 2530 GSM945321 Stam UW DS14121 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa14dPkRep1 diffProtA_14d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 14 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa9dPkRep2 H7ES H3K4M3 Pk 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002542 2542 GSM945190 Stam UW DS14705 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa9dPkRep2 diffProtA_9d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 9 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa9dPkRep1 H7ES H3K4M3 Pk 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002542 2542 GSM945190 Stam UW DS14706 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa9dPkRep1 diffProtA_9d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 9 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa5dPkRep2 H7ES H3K4M3 Pk 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002531 2531 GSM945322 Stam UW DS14116 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa5dPkRep2 diffProtA_5d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 5 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa5dPkRep1 H7ES H3K4M3 Pk 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-04-04 2013-01-04 wgEncodeEH002531 2531 GSM945322 Stam UW DS13777 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa5dPkRep1 diffProtA_5d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 5 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa2dPkRep2 H7ES H3K4M3 Pk 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002541 2541 GSM945191 Stam UW DS14703 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa2dPkRep2 diffProtA_2d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 2 d Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa2dPkRep1 H7ES H3K4M3 Pk 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002541 2541 GSM945191 Stam UW DS14704 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa2dPkRep1 diffProtA_2d Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm Regions of enriched signal in experiment H7-hESC H3K4me3 diffProtA 2 d Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12875H3k04me3StdPkRep1 GM75 H3K4M3 Pk 1 H3K4me3 GM12875 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002041 2041 GSM945221 Stam UW DS18910 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneGm12875H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12875 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865H3k04me3StdPkRep2 GM65 H3K4M3 Pk 2 H3K4me3 GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002039 2039 GSM945295 Stam UW DS20810 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneGm12865H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865H3k04me3StdPkRep1 GM65 H3K4M3 Pk 1 H3K4me3 GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002039 2039 GSM945295 Stam UW DS18707 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneGm12865H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12865 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864H3k04me3StdPkRep2 GM64 H3K4M3 Pk 2 H3K4me3 GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002038 2038 GSM945296 Stam UW DS18900 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneGm12864H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864H3k04me3StdPkRep1 GM64 H3K4M3 Pk 1 H3K4me3 GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002038 2038 GSM945296 Stam UW DS18706 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneGm12864H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12864 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k36me3StdPkRep2 GM90 H3K36M3 Pk 2 H3K36me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000444 444 GSM945213 Stam UW DS12189 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneGm06990H3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k36me3StdPkRep1 GM90 H3K36M3 Pk 1 H3K36me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-22 2010-07-21 wgEncodeEH000444 444 GSM945213 Stam UW DS12192 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneGm06990H3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k27me3StdPkRep2 GM90 H3K27M3 Pk 2 H3K27me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2010-06-11 2011-03-11 wgEncodeEH000427 427 GSM945205 Stam UW DS12188 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneGm06990H3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k27me3StdPkRep1 GM90 H3K27M3 Pk 1 H3K27me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000427 427 GSM945205 Stam UW DS12191 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneGm06990H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k4me3StdPkRep2 GM90 H3K4M3 Pk 2 H3K4me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2010-06-11 2011-03-11 wgEncodeEH000417 417 GSM945179 Stam UW DS11519 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneGm06990H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k4me3StdPkRep1 GM90 H3K4M3 Pk 1 H3K4me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-13 2010-07-12 wgEncodeEH000417 417 GSM945179 Stam UW DS11521 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneGm06990H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM06990 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k36me3StdPkRep2 Caco H3K36M3 Pk 2 H3K36me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2010-06-11 2011-03-11 wgEncodeEH000426 426 GSM945206 Stam UW DS12405 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneCaco2H3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k36me3StdPkRep1 Caco H3K36M3 Pk 1 H3K36me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000426 426 GSM945206 Stam UW DS12406 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneCaco2H3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k27me3StdPkRep2 Caco H3K27M3 Pk 2 H3K27me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000425 425 GSM945203 Stam UW DS12218 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneCaco2H3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k27me3StdPkRep1 Caco H3K27M3 Pk 1 H3K27me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-20 2010-07-20 wgEncodeEH000425 425 GSM945203 Stam UW DS12221 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneCaco2H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k4me3StdPkRep2 Caco H3K4M3 Pk 2 H3K4me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2010-06-11 2011-03-11 wgEncodeEH000407 407 GSM945162 Stam UW DS11785 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneCaco2H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k4me3StdPkRep1 Caco H3K4M3 Pk 1 H3K4me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-09-29 2010-06-29 wgEncodeEH000407 407 GSM945162 Stam UW DS11784 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneCaco2H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Caco-2 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k36me3StdPkRep2 BJ H3K36M3 Pk 2 H3K36me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000443 443 GSM945207 Stam UW DS12195 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneBjH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k36me3StdPkRep1 BJ H3K36M3 Pk 1 H3K36me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-22 2010-07-21 wgEncodeEH000443 443 GSM945207 Stam UW DS12198 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneBjH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k27me3StdPkRep2 BJ H3K27M3 Pk 2 H3K27me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-09 wgEncodeEH000424 424 GSM945204 Stam UW DS12197 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneBjH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k27me3StdPkRep1 BJ H3K27M3 Pk 1 H3K27me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000424 424 GSM945204 Stam UW DS12194 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneBjH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k4me3StdPkRep2 BJ H3K4M3 Pk 2 H3K4me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000416 416 GSM945178 Stam UW DS11561 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneBjH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k4me3StdPkRep1 BJ H3K4M3 Pk 1 H3K4me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-13 2010-07-12 wgEncodeEH000416 416 GSM945178 Stam UW DS11563 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneBjH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BJ H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cH3k04me3StdPkRep2 BE2_C H3K4M3 Pk 2 H3K4me3 BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001906 1906 GSM945241 Stam UW DS18310 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneBe2cH3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BE2_C H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cH3k04me3StdPkRep1 BE2_C H3K4M3 Pk 1 H3K4me3 BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001906 1906 GSM945241 Stam UW DS18309 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneBe2cH3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment BE2_C H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafH3k4me3StdPkRep2 AoAF H3K4M3 Pk 2 H3K4me3 AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000937 937 GSM945170 Stam UW DS15747 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAoafH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafH3k4me3StdPkRep1 AoAF H3K4M3 Pk 1 H3K4me3 AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000937 937 GSM945170 Stam UW DS15746 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAoafH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AoAF H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803H3k4me3StdPkRep2 AG03 H3K4M3 Pk 2 H3K4me3 AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000935 935 GSM945172 Stam UW DS15745 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAg10803H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG10803 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803H3k4me3StdPkRep1 AG03 H3K4M3 Pk 1 H3K4me3 AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000935 935 GSM945172 Stam UW DS15744 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg10803H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG10803 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319H3k4me3StdPkRep2 AG19 H3K4M3 Pk 2 H3K4me3 AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000933 933 GSM945166 Stam UW DS15743 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAg09319H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09319 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319H3k4me3StdPkRep1 AG19 H3K4M3 Pk 1 H3K4me3 AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000933 933 GSM945166 Stam UW DS15742 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg09319H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09319 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309H3k4me3StdPkRep2 AG09 H3K4M3 Pk 2 H3K4me3 AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000931 931 GSM945168 Stam UW DS16033 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAg09309H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09309 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309H3k4me3StdPkRep1 AG09 H3K4M3 Pk 1 H3K4me3 AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000931 931 GSM945168 Stam UW DS16034 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg09309H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG09309 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k27me3StdPkRep1 AG50 H3K27m3 Pk 1 H3K27me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003036 3036 GSM1010913 Stam UW DS21480 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg04450H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k27acStdPkRep1 AG50 H3K27ac Pk 1 H3K27ac AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003035 3035 GSM1010912 Stam UW DS21479 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg04450H3k27acStdPkRep1 None Peaks Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 H3K27ac Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k09me3StdPkRep2 AG50 H3K9me3 Pk 2 H3K9me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003037 3037 GSM1010914 Stam UW DS21481 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAg04450H3k09me3StdPkRep2 None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 H3K9me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k09me3StdPkRep1 AG50 H3K9me3 Pk 1 H3K9me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003037 3037 GSM1010914 Stam UW DS21482 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg04450H3k09me3StdPkRep1 None Peaks Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 H3K9me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k4me3StdPkRep2 AG50 H3K4M3 Pk 2 H3K4me3 AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000929 929 GSM945177 Stam UW DS15741 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAg04450H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k4me3StdPkRep1 AG50 H3K4M3 Pk 1 H3K4me3 AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000929 929 GSM945177 Stam UW DS15740 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg04450H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04450 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449H3k4me3StdPkRep2 AG49 H3K4M3 Pk 2 H3K4me3 AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000927 927 GSM945187 Stam UW DS15739 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneAg04449H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04449 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449H3k4me3StdPkRep1 AG49 H3K4M3 Pk 1 H3K4me3 AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000927 927 GSM945187 Stam UW DS15737 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneAg04449H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment AG04449 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746H3k27me3StdPkRep1 CD14 H3K27M3 Pk 1 H3K27me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002167 2167 GSM945301 Stam UW DS19094 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneMonocd14ro1746H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Monocytes-CD14+ RO 01746 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746H3k04me3StdPkRep1 CD14 H3K4M3 Pk 1 H3K4me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002168 2168 GSM945225 Stam UW DS18981 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneMonocd14ro1746H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment Monocytes-CD14+ RO 01746 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7H3k04me3StdPkRep2 MCF7 H3K4M3 Pk 2 H3K4me3 MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000967 967 GSM945269 Stam UW DS16201 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneMcf7H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7H3k4me3StdPkRep1 MCF7 H3K4M3 Pk 1 H3K4me3 MCF-7 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000967 967 GSM945269 Stam UW DS16202 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneMcf7H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment MCF-7 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k36me3StdPkRep2 HUVE H3K36M3 Pk 2 H3K36me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000431 431 GSM945233 Stam UW DS12225 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHuvecH3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k36me3StdPkRep1 HUVE H3K36M3 Pk 1 H3K36me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000431 431 GSM945233 Stam UW DS12228 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHuvecH3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k27me3StdPkRep2 HUVE H3K27M3 Pk 2 H3K27me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000411 411 GSM945180 Stam UW DS12224 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHuvecH3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k27me3StdPkRep1 HUVE H3K27M3 Pk 1 H3K27me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000411 411 GSM945180 Stam UW DS12227 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHuvecH3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k4me3StdPkRep2 HUVE H3K4M3 Pk 2 H3K4me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000412 412 GSM945181 Stam UW DS11458 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHuvecH3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k4me3StdPkRep1 HUVE H3K4M3 Pk 1 H3K4me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000412 412 GSM945181 Stam UW DS11460 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHuvecH3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HUVEC H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k36me3StdPkRep2 HepG H3K36M3 Pk 2 H3K36me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000446 446 GSM945211 Stam UW DS12075 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHepg2H3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k36me3StdPkRep1 HepG H3K36M3 Pk 1 H3K36me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-22 2010-07-21 wgEncodeEH000446 446 GSM945211 Stam UW DS12207 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHepg2H3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k27me3StdPkRep2 HepG H3K27M3 Pk 2 H3K27me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000433 433 GSM945231 Stam UW DS12206 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHepg2H3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k27me3StdPkRep1 HepG H3K27M3 Pk 1 H3K27me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000433 433 GSM945231 Stam UW DS12076 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHepg2H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k4me3StdPkRep2 HepG H3K4M3 Pk 2 H3K4me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000413 413 GSM945182 Stam UW DS11780 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHepg2H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k4me3StdPkRep1 HepG H3K4M3 Pk 1 H3K4me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-09-29 2010-06-29 wgEncodeEH000413 413 GSM945182 Stam UW DS11781 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHepg2H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HepG2 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k36me3StdPkRep2 HeLa H3K36M3 Pk 2 H3K36me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000432 432 GSM945230 Stam UW DS12201 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHelas3H3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k36me3StdPkRep1 HeLa H3K36M3 Pk 1 H3K36me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000432 432 GSM945230 Stam UW DS12071 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHelas3H3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k27me3StdPkRep2 HeLa H3K27M3 Pk 2 H3K27me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000442 442 GSM945208 Stam UW DS12070 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHelas3H3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k27me3StdPkRep1 HeLa H3K27M3 Pk 1 H3K27me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000442 442 GSM945208 Stam UW DS12072 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHelas3H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k4me3StdPkRep2 HeLa H3K4M3 Pk 2 H3K4me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000423 423 GSM945201 Stam UW DS11553 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneHelas3H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k4me3StdPkRep1 HeLa H3K4M3 Pk 1 H3K4me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-13 2010-07-12 wgEncodeEH000423 423 GSM945201 Stam UW DS11555 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneHelas3H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment HeLa-S3 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01794H3k04me3StdPkRep3 20+94 H3K4M3 Pk 3 H3K4me3 CD20+_RO01794 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEH002171 2171 GSM945198 Stam UW DS18983 lmax-v1.0 hg19 3 exp wgEncodeUwHistoneCd20ro01794H3k04me3StdPkRep3 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CD20+ (RO 01794) H3K4me3 Histone Mod ChIP-seq Peaks 3 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778H3k04me3StdPkRep2 20+78 H3K4M3 Pk 2 H3K4me3 CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002166 2166 GSM945229 Stam UW DS18986 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneCd20ro01778H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CD20+ (RO 01778) H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778H3k04me3StdPkRep1 20+78 H3K4M3 Pk 1 H3K4me3 CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-14 2012-06-14 wgEncodeEH002166 2166 GSM945229 Stam UW DS18985 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneCd20ro01778H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment CD20+ (RO 01778) H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549H3k04me3StdPkRep2 A549 H3K4M3 Pk 2 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001905 1905 GSM945244 Stam UW DS18304 lmax-v1.0 hg19 2 exp wgEncodeUwHistoneA549H3k04me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment A549 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549H3k04me3StdPkRep1 A549 H3K4M3 Pk 1 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001905 1905 GSM945244 Stam UW DS18305 lmax-v1.0 hg19 1 exp wgEncodeUwHistoneA549H3k04me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment A549 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k36me3StdPkRep2 K562 H3K36M3 Pk 2 H3K36me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000435 435 GSM945302 Stam UW DS12177 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneK562H3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k36me3StdPkRep1 K562 H3K36M3 Pk 1 H3K36me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000435 435 GSM945302 Stam UW DS12067 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneK562H3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k27me3StdPkRep2 K562 H3K27M3 Pk 2 H3K27me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000434 434 GSM945228 Stam UW DS12068 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneK562H3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k27me3StdPkRep1 K562 H3K27M3 Pk 1 H3K27me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000434 434 GSM945228 Stam UW DS12066 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneK562H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k4me3StdPkRep2 K562 H3K4M3 Pk 2 H3K4me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000400 400 GSM945165 Stam UW DS11509 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneK562H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k4me3StdPkRep1 K562 H3K4M3 Pk 1 H3K4me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000400 400 GSM945165 Stam UW DS11507 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneK562H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment K562 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k36me3StdPkRep2 GM78 H3K36M3 Pk 2 H3K36me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000445 445 GSM945212 Stam UW DS12183 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneGm12878H3k36me3StdPkRep2 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 H3K36me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k36me3StdPkRep1 GM78 H3K36M3 Pk 1 H3K36me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-22 2010-07-21 wgEncodeEH000445 445 GSM945212 Stam UW DS12186 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneGm12878H3k36me3StdPkRep1 None Peaks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 H3K36me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k27me3StdPkRep2 GM78 H3K27M3 Pk 2 H3K27me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000428 428 GSM945196 Stam UW DS12185 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneGm12878H3k27me3StdPkRep2 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 H3K27me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k27me3StdPkRep1 GM78 H3K27M3 Pk 1 H3K27me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000428 428 GSM945196 Stam UW DS12182 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneGm12878H3k27me3StdPkRep1 None Peaks Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 H3K27me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k4me3StdPkRep2 GM78 H3K4M3 Pk 2 H3K4me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-06-30 2010-03-29 wgEncodeEH000395 395 GSM945188 Stam UW DS11511 lmax-v1.0 hg18 2 exp wgEncodeUwHistoneGm12878H3k4me3StdPkRep2 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 H3K4me3 Histone Mod ChIP-seq Peaks 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k4me3StdPkRep1 GM78 H3K4M3 Pk 1 H3K4me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-06-30 2010-03-29 wgEncodeEH000395 395 GSM945188 Stam UW DS11513 lmax-v1.0 hg18 1 exp wgEncodeUwHistoneGm12878H3k4me3StdPkRep1 None Peaks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Regions of enriched signal in experiment GM12878 H3K4me3 Histone Mod ChIP-seq Peaks 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneViewHot Hotspots Histone Modifications by ChIP-seq from ENCODE/University of Washington Regulation 
wgEncodeUwHistoneWi38H3k04me3StdHotspotsRep2 WI38 H3K4M3 Ht 2 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001914 1914 GSM945265 Stam UW DS18349 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneWi38H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3StdHotspotsRep1 WI38 H3K4M3 Ht 1 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001914 1914 GSM945265 Stam UW DS18350 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneWi38H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3OhtamStdHotspotsRep2 WI38 H3K4M3 Ht 2 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002047 2047 GSM945215 Stam UW DS18354 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneWi38H3k04me3OhtamStdHotspotsRep2 4OHTAM_20nM_72hr Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 H3K4me3 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWi38H3k04me3OhtamStdHotspotsRep1 WI38 H3K4M3 Ht 1 H3K4me3 WI-38 std ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEH002047 2047 GSM945215 Stam UW DS18355 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneWi38H3k04me3OhtamStdHotspotsRep1 4OHTAM_20nM_72hr Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic lung fibroblast cells, hTERT immortalized, includes Raf1 construct Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington 72 hours with 20 nM 4-hydroxytamoxifen (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm WI-38 H3K4me3 4-OHTAM 20 nM 72 hr Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1H3k04me3StdHotspotsRep2 WERI H3K4M3 Ht 2 H3K4me3 WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001913 1913 GSM945263 Stam UW DS16213 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneWerirb1H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WERI-Rb-1 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneWerirb1H3k04me3StdHotspotsRep1 WERI H3K4M3 Ht 1 H3K4me3 WERI-Rb-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001913 1913 GSM945263 Stam UW DS16214 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneWerirb1H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinoblastoma (PMID: 844036) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm WERI-Rb-1 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k36me3StdHotspotsRep2 SKRA H3K36M3 Ht 2 H3K36me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000441 441 GSM945209 Stam UW DS12403 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneSknshraH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k36me3StdHotspotsRep1 SKRA H3K36M3 Ht 1 H3K36me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000441 441 GSM945209 Stam UW DS12404 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneSknshraH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k27me3StdHotspotsRep2 SKRA H3K27M3 Ht 2 H3K27me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-20 2010-07-20 wgEncodeEH000440 440 GSM945210 Stam UW DS12215 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneSknshraH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k27me3StdHotspotsRep1 SKRA H3K27M3 Ht 1 H3K27me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000440 440 GSM945210 Stam UW DS12212 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneSknshraH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k4me3StdHotspotsRep2 SKRA H3K4M3 Ht 2 H3K4me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000422 422 GSM945202 Stam UW DS11783 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneSknshraH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknshraH3k4me3StdHotspotsRep1 SKRA H3K4M3 Ht 1 H3K4me3 SK-N-SH_RA std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000422 422 GSM945202 Stam UW DS11782 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneSknshraH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-SH_RA H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcH3k04me3StdHotspotsRep2 SKNMC H3K4M3 Ht 2 H3K4me3 SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001912 1912 GSM945264 Stam UW DS18345 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneSknmcH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-MC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSknmcH3k04me3StdHotspotsRep1 SKNMC H3K4M3 Ht 1 H3K4me3 SK-N-MC std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001912 1912 GSM945264 Stam UW DS18344 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneSknmcH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SK-N-MC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcH3k04me3StdHotspotsRep2 SKMC H3K4M3 Ht 2 H3K4me3 SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002046 2046 GSM945214 Stam UW DS16212 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneSkmcH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SKMC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSkmcH3k04me3StdHotspotsRep1 SKMC H3K4M3 Ht 1 H3K4me3 SKMC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002046 2046 GSM945214 Stam UW DS16211 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneSkmcH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skeletal muscle cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SKMC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k36me3StdHotspotsRep2 SAEC H3K36M3 Ht 2 H3K36me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000438 438 GSM945226 Stam UW DS12246 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneSaecH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k36me3StdHotspotsRep1 SAEC H3K36M3 Ht 1 H3K36me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000438 438 GSM945226 Stam UW DS12243 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneSaecH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k27me3StdHotspotsRep2 SAEC H3K27M3 Ht 2 H3K27me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000420 420 GSM945200 Stam UW DS12245 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneSaecH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k27me3StdHotspotsRep1 SAEC H3K27M3 Ht 1 H3K27me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000420 420 GSM945200 Stam UW DS12242 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneSaecH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k4me3StdHotspotsRep2 SAEC H3K4M3 Ht 2 H3K4me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000421 421 GSM945199 Stam UW DS11579 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneSaecH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneSaecH3k4me3StdHotspotsRep1 SAEC H3K4M3 Ht 1 H3K4me3 SAEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000421 421 GSM945199 Stam UW DS11577 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneSaecH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. small airway epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm SAEC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecH3k04me3StdHotspotsRep2 RPTEC H3K4M3 Ht 2 H3K4me3 RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002044 2044 GSM945216 Stam UW DS18339 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneRptecH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm RPTEC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneRptecH3k04me3StdHotspotsRep1 RPTEC H3K4M3 Ht 1 H3K4me3 RPTEC std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002044 2044 GSM945216 Stam UW DS18340 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneRptecH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal proximal tubule epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm RPTEC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1H3k04me3StdHotspotsRep2 PANC1 H3K4M3 Ht 2 H3K4me3 PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001911 1911 GSM945261 Stam UW DS18334 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistonePanc1H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm PANC-1 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistonePanc1H3k04me3StdHotspotsRep1 PANC1 H3K4M3 Ht 1 H3K4me3 PANC-1 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001911 1911 GSM945261 Stam UW DS18335 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistonePanc1H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pancreatic carcinoma, (PMID: 1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm PANC-1 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfH3k04me3StdHotspotsRep2 NHLF H3K4M3 Ht 2 H3K4me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001910 1910 GSM945262 Stam UW DS16350 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneNhlfH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHLF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhlfH3k04me3StdHotspotsRep1 NHLF H3K4M3 Ht 1 H3K4me3 NHLF std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001910 1910 GSM945262 Stam UW DS16351 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneNhlfH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. lung fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHLF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k36me3StdHotspotsRep2 NHEK H3K36M3 Ht 2 H3K36me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000414 414 GSM945174 Stam UW DS12240 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneNhekH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k36me3StdHotspotsRep1 NHEK H3K36M3 Ht 1 H3K36me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000414 414 GSM945174 Stam UW DS12237 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneNhekH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k27me3StdHotspotsRep2 NHEK H3K27M3 Ht 2 H3K27me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000436 436 GSM945300 Stam UW DS12080 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneNhekH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k27me3StdHotspotsRep1 NHEK H3K27M3 Ht 1 H3K27me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000436 436 GSM945300 Stam UW DS12078 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneNhekH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k4me3StdHotspotsRep2 NHEK H3K4M3 Ht 2 H3K4me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-13 2010-07-12 wgEncodeEH000415 415 GSM945175 Stam UW DS11557 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneNhekH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhekH3k4me3StdHotspotsRep1 NHEK H3K4M3 Ht 1 H3K4me3 NHEK std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000415 415 GSM945175 Stam UW DS11559 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneNhekH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epidermal keratinocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHEK H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoH3k4me3StdHotspotsRep2 NHDF H3K4M3 Ht 2 H3K4me3 NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000971 971 GSM945251 Stam UW DS16207 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneNhdfneoH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-neo H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneNhdfneoH3k4me3StdHotspotsRep1 NHDF H3K4M3 Ht 1 H3K4me3 NHDF-neo std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000971 971 GSM945251 Stam UW DS16206 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneNhdfneoH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neonatal dermal fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NHDF-neo H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneNb4H3k4me3StdHotspotsRep1 NB4 H3K4M3 Ht 1 H3K4me3 NB4 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000969 969 GSM945275 Stam UW DS16346 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneNb4H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. acute promyelocytic leukemia cell line. (PMID: 1995093) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm NB4 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapH3k04me3StdHotspotsRep2 LNCP H3K4M3 Ht 2 H3K4me3 LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001909 1909 GSM945240 Stam UW DS18329 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneLncapH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm LNCaP H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneLncapH3k04me3StdHotspotsRep1 LNCP H3K4M3 Ht 1 H3K4me3 LNCaP std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001909 1909 GSM945240 Stam UW DS18330 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneLncapH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm LNCaP H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatH3k4me3StdHotspotsRep2 Jurk H3K4M3 Ht 2 H3K4me3 Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000965 965 GSM945267 Stam UW DS16196 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneJurkatH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Jurkat H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneJurkatH3k4me3StdHotspotsRep1 Jurk H3K4M3 Ht 1 H3K4me3 Jurkat std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000965 965 GSM945267 Stam UW DS16197 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneJurkatH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID: 68013) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Jurkat H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfH3k4me3StdHotspotsRep2 HVMF H3K4M3 Ht 2 H3K4me3 HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000963 963 GSM945273 Stam UW DS16155 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHvmfH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HVMF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHvmfH3k4me3StdHotspotsRep1 HVMF H3K4M3 Ht 1 H3K4me3 HVMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000963 963 GSM945273 Stam UW DS16156 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHvmfH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. villous mesenchymal fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HVMF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeH3k4me3StdHotspotsRep2 HRPE H3K4M3 Ht 2 H3K4me3 HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000961 961 GSM945271 Stam UW DS16188 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHrpeH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRPEpIC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHrpeH3k4me3StdHotspotsRep1 HRPE H3K4M3 Ht 1 H3K4me3 HRPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000961 961 GSM945271 Stam UW DS16189 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHrpeH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. retinal pigment epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRPEpIC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k36me3StdHotspotsRep2 HRE H3K36M3 Ht 2 H3K36me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000430 430 GSM945232 Stam UW DS12418 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHreH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k36me3StdHotspotsRep1 HRE H3K36M3 Ht 1 H3K36me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000430 430 GSM945232 Stam UW DS12234 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHreH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k27me3StdHotspotsRep2 HRE H3K27M3 Ht 2 H3K27me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000429 429 GSM945160 Stam UW DS12415 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHreH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k27me3StdHotspotsRep1 HRE H3K27M3 Ht 1 H3K27me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000429 429 GSM945160 Stam UW DS12422 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHreH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k4me3StdHotspotsRep2 HRE H3K4M3 Ht 2 H3K4me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-13 2010-07-12 wgEncodeEH000409 409 GSM945276 Stam UW DS11573 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHreH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHreH3k4me3StdHotspotsRep1 HRE H3K4M3 Ht 1 H3K4me3 HRE std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000409 409 GSM945276 Stam UW DS11575 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHreH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. renal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HRE H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfH3k4me3StdHotspotsRep2 HPF H3K4M3 Ht 2 H3K4me3 HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000959 959 GSM945284 Stam UW DS16183 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHpfH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpfH3k4me3StdHotspotsRep1 HPF H3K4M3 Ht 1 H3K4me3 HPF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000959 959 GSM945284 Stam UW DS16184 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHpfH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary fibroblasts isolated from lung tissue Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafH3k4me3StdHotspotsRep2 HPAF H3K4M3 Ht 2 H3K4me3 HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000957 957 GSM945292 Stam UW DS16154 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHpafH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPAF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHpafH3k4me3StdHotspotsRep1 HPAF H3K4M3 Ht 1 H3K4me3 HPAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000957 957 GSM945292 Stam UW DS16153 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHpafH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. pulmonary artery fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HPAF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfH3k4me3StdHotspotsRep2 HMF H3K4M3 Ht 2 H3K4me3 HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000955 955 GSM945290 Stam UW DS16152 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHmfH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmfH3k4me3StdHotspotsRep1 HMF H3K4M3 Ht 1 H3K4me3 HMF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000955 955 GSM945290 Stam UW DS16151 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHmfH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k27me3StdHotspotsRep1 HMEC H3K27M3 Ht 1 H3K27me3 HMEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000408 408 GSM945277 Stam UW DS12082 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHmecH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMEC H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k4me3StdHotspotsRep2 HMEC H3K4M3 Ht 2 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000954 954 GSM945159 Stam UW DS15761 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHmecH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMEC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHmecH3k4me3StdHotspotsRep1 HMEC H3K4M3 Ht 1 H3K4me3 HMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000954 954 GSM945159 Stam UW DS15762 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHmecH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HMEC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60H3k4me3StdHotspotsRep2 HL-60 H3K4M3 Ht 2 H3K4me3 HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000418 418 GSM945222 Stam UW DS11797 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHl60H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HL-60 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHl60H3k4me3StdHotspotsRep1 HL-60 H3K4M3 Ht 1 H3K4me3 HL-60 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-11 wgEncodeEH000418 418 GSM945222 Stam UW DS11795 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHl60H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. promyelocytic leukemia cells, (PMID: 276884) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HL-60 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycH3k04me3StdHotspotsRep2 HFMc H3K4M3 Ht 2 H3K4me3 HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001908 1908 GSM945239 Stam UW DS18325 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneHffmycH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFFMyc H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffmycH3k04me3StdHotspotsRep1 HFMc H3K4M3 Ht 1 H3K4me3 HFF-Myc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001908 1908 GSM945239 Stam UW DS18324 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneHffmycH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast cells expressing canine cMyc Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFFMyc H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHffH3k04me3StdHotspotsRep1 HFF H3K4M3 Ht 1 H3K4me3 HFF std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002042 2042 GSM945218 Stam UW DS18320 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneHffH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. foreskin fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HFF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293H3k4me3StdHotspotsRep2 HEK H3K4M3 Ht 2 H3K4me3 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000953 953 GSM945288 Stam UW DS15759 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHek293H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEK293 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHek293H3k4me3StdHotspotsRep1 HEK H3K4M3 Ht 1 H3K4me3 HEK293 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000953 953 GSM945288 Stam UW DS15760 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHek293H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEK293 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeH3k4me3StdHotspotsRep2 HEE H3K4M3 Ht 2 H3K4me3 HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000951 951 GSM945286 Stam UW DS16061 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHeeH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEEpIC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHeeH3k4me3StdHotspotsRep1 HEE H3K4M3 Ht 1 H3K4me3 HEEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000951 951 GSM945286 Stam UW DS16060 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHeeH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. esophageal epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HEEpIC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116H3k4me3StdHotspotsRep2 HCT16 H3K4M3 Ht 2 H3K4me3 HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000949 949 GSM945304 Stam UW DS16055 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHct116H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCT-116 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHct116H3k4me3StdHotspotsRep1 HCT16 H3K4M3 Ht 1 H3K4me3 HCT-116 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000949 949 GSM945304 Stam UW DS16056 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHct116H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal carcinoma (PMID: 7214343) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCT-116 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeH3k4me3StdHotspotsRep2 HCPE H3K4M3 Ht 2 H3K4me3 HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000947 947 GSM945306 Stam UW DS15757 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHcpeH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCPEpiC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcpeH3k4me3StdHotspotsRep1 HCPE H3K4M3 Ht 1 H3K4me3 HCPEpiC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000947 947 GSM945306 Stam UW DS15758 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHcpeH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. choroid plexus epithelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCPEpiC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmH3k4me3StdHotspotsRep2 HCM H3K4M3 Ht 2 H3K4me3 HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000945 945 GSM945308 Stam UW DS15756 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHcmH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCM H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcmH3k4me3StdHotspotsRep1 HCM H3K4M3 Ht 1 H3K4me3 HCM std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000945 945 GSM945308 Stam UW DS15755 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHcmH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac myocytes Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCM H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfaaH3k4me3StdHotspotsRep1 HCFa H3K4M3 Ht 1 H3K4me3 HCFaa std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000943 943 GSM945310 Stam UW DS15754 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHcfaaH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts- adult atrial Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCFaa H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfH3k4me3StdHotspotsRep2 HCF H3K4M3 Ht 2 H3K4me3 HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000941 941 GSM945312 Stam UW DS15753 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHcfH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHcfH3k4me3StdHotspotsRep1 HCF H3K4M3 Ht 1 H3K4me3 HCF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000941 941 GSM945312 Stam UW DS15751 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHcfH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cardiac fibroblasts Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HCF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecH3k4me3StdHotspotsRep2 HBMEC H3K4M3 Ht 2 H3K4me3 HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000939 939 GSM945163 Stam UW DS15748 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHbmecH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBMEC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHbmecH3k4me3StdHotspotsRep1 HBMEC H3K4M3 Ht 1 H3K4me3 HBMEC std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000939 939 GSM945163 Stam UW DS15749 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHbmecH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. brain microvascular endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HBMEC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspH3k4me3StdHotspotsRep2 HAsp H3K4M3 Ht 2 H3K4me3 HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000973 973 GSM945249 Stam UW DS16045 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHaspH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HA-sp H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHaspH3k4me3StdHotspotsRep1 HAsp H3K4M3 Ht 1 H3K4me3 HA-sp std ChipSeq ENCODE Jan 2011 Freeze 2010-10-28 2011-07-28 wgEncodeEH000973 973 GSM945249 Stam UW DS16044 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneHaspH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes spinal cord Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HA-sp H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacH3k04me3StdHotspotsRep2 HAc H3K4M3 Ht 2 H3K4me3 HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001907 1907 GSM945242 Stam UW DS18314 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneHacH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAc H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHacH3k04me3StdHotspotsRep1 HAc H3K4M3 Ht 1 H3K4me3 HAc std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001907 1907 GSM945242 Stam UW DS18315 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneHacH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. astrocytes-cerebellar Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HAc H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdHotspotsRep2 H7ES H3K36M3 Ht 2 H3K36me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000924 924 GSM945184 Stam UW DS14114 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdHotspotsRep1 H7ES H3K36M3 Ht 1 H3K36me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000924 924 GSM945184 Stam UW DS14115 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa14dHotspotsRep2 H7ES H3K36M3 Ht 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002537 2537 GSM945324 Stam UW DS14650 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa14dHotspotsRep2 diffProtA_14d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 14 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa14dHotspotsRep1 H7ES H3K36M3 Ht 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002537 2537 GSM945324 Stam UW DS14123 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa14dHotspotsRep1 diffProtA_14d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 14 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa9dHotspotsRep2 H7ES H3K36M3 Ht 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002540 2540 GSM945192 Stam UW DS15386 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa9dHotspotsRep2 diffProtA_9d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 9 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa9dHotspotsRep1 H7ES H3K36M3 Ht 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002540 2540 GSM945192 Stam UW DS14648 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa9dHotspotsRep1 diffProtA_9d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 9 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa5dHotspotsRep2 H7ES H3K36M3 Ht 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002539 2539 GSM945316 Stam UW DS14120 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa5dHotspotsRep2 diffProtA_5d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 5 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa5dHotspotsRep1 H7ES H3K36M3 Ht 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002539 2539 GSM945316 Stam UW DS14119 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa5dHotspotsRep1 diffProtA_5d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 5 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa2dHotspotsRep2 H7ES H3K36M3 Ht 2 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002538 2538 GSM945315 Stam UW DS14646 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa2dHotspotsRep2 diffProtA_2d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 2 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k36me3StdDiffa2dHotspotsRep1 H7ES H3K36M3 Ht 1 H3K36me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002538 2538 GSM945315 Stam UW DS15385 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k36me3StdDiffa2dHotspotsRep1 diffProtA_2d Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K36me3 diffProtA 2 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdHotspotsRep2 H7ES H3K27M3 Ht 2 H3K27me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000923 923 GSM945183 Stam UW DS14113 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdHotspotsRep1 H7ES H3K27M3 Ht 1 H3K27me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000923 923 GSM945183 Stam UW DS13428 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa14dHotspotsRep2 H7ES H3K27M3 Ht 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002533 2533 GSM945320 Stam UW DS14122 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa14dHotspotsRep2 diffProtA_14d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 14 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa14dHotspotsRep1 H7ES H3K27M3 Ht 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002533 2533 GSM945320 Stam UW DS14649 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa14dHotspotsRep1 diffProtA_14d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 14 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa9dHotspotsRep2 H7ES H3K27M3 Ht 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002536 2536 GSM945323 Stam UW DS14709 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa9dHotspotsRep2 diffProtA_9d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 9 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa9dHotspotsRep1 H7ES H3K27M3 Ht 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002536 2536 GSM945323 Stam UW DS14647 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa9dHotspotsRep1 diffProtA_9d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 9 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa5dHotspotsRep2 H7ES H3K27M3 Ht 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002535 2535 GSM945326 Stam UW DS14118 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa5dHotspotsRep2 diffProtA_5d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 5 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa5dHotspotsRep1 H7ES H3K27M3 Ht 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002535 2535 GSM945326 Stam UW DS13778 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa5dHotspotsRep1 diffProtA_5d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 5 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa2dHotspotsRep2 H7ES H3K27M3 Ht 2 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002534 2534 GSM945325 Stam UW DS14708 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa2dHotspotsRep2 diffProtA_2d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 2 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k27me3StdDiffa2dHotspotsRep1 H7ES H3K27M3 Ht 1 H3K27me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002534 2534 GSM945325 Stam UW DS14645 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k27me3StdDiffa2dHotspotsRep1 diffProtA_2d Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K27me3 diffProtA 2 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k4me3StdHotspotsRep2 H7ES H3K4M3 Ht 2 H3K4me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000925 925 GSM945185 Stam UW DS14112 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneH7esH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k4me3StdHotspotsRep1 H7ES H3K4M3 Ht 1 H3K4me3 H7-hESC std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000925 925 GSM945185 Stam UW DS13427 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneH7esH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa14dHotspotsRep2 H7ES H3K4M3 Ht 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-04-04 2013-01-04 wgEncodeEH002530 2530 GSM945321 Stam UW DS14707 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa14dHotspotsRep2 diffProtA_14d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 14 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa14dHotspotsRep1 H7ES H3K4M3 Ht 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002530 2530 GSM945321 Stam UW DS14121 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa14dHotspotsRep1 diffProtA_14d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 14 days, cell sorting and specific growth factors were used, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 14 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa9dHotspotsRep2 H7ES H3K4M3 Ht 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002542 2542 GSM945190 Stam UW DS14705 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa9dHotspotsRep2 diffProtA_9d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 9 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa9dHotspotsRep1 H7ES H3K4M3 Ht 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002542 2542 GSM945190 Stam UW DS14706 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa9dHotspotsRep1 diffProtA_9d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 9 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 9 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa5dHotspotsRep2 H7ES H3K4M3 Ht 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002531 2531 GSM945322 Stam UW DS14116 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa5dHotspotsRep2 diffProtA_5d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 5 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa5dHotspotsRep1 H7ES H3K4M3 Ht 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2012-04-04 2013-01-04 wgEncodeEH002531 2531 GSM945322 Stam UW DS13777 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa5dHotspotsRep1 diffProtA_5d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 5 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 5 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa2dHotspotsRep2 H7ES H3K4M3 Ht 2 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002541 2541 GSM945191 Stam UW DS14703 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa2dHotspotsRep2 diffProtA_2d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 2 d Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneH7esH3k04me3StdDiffa2dHotspotsRep1 H7ES H3K4M3 Ht 1 H3K4me3 H7-hESC std ChipSeq ENCODE Mar 2012 Freeze 2011-12-13 2012-09-12 wgEncodeEH002541 2541 GSM945191 Stam UW DS14704 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneH7esH3k04me3StdDiffa2dHotspotsRep1 diffProtA_2d Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. undifferentiated embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington H7 embryoid bodies differentiation protocol for cardiomyocyte, endothelial, smooth muscle, with markers cardiac troponin T (cTnT), CD31/PECAM1, smooth muscle alpha actin (SMA), respectively, using proteins from bone morphogenic protein 4 (BMP4), activin A and basic fibroblast growth factor (bFGF) for 2 days, lineage: mesoderm ChIP-seq affinity zones identified using the HotSpot algorithm H7-hESC H3K4me3 diffProtA 2 d Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12875H3k04me3StdHotspotsRep1 GM75 H3K4M3 Ht 1 H3K4me3 GM12875 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002041 2041 GSM945221 Stam UW DS18910 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneGm12875H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12875 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865H3k04me3StdHotspotsRep2 GM65 H3K4M3 Ht 2 H3K4me3 GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-12-12 2012-09-12 wgEncodeEH002039 2039 GSM945295 Stam UW DS20810 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneGm12865H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12865H3k04me3StdHotspotsRep1 GM65 H3K4M3 Ht 1 H3K4me3 GM12865 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002039 2039 GSM945295 Stam UW DS18707 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneGm12865H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12865 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864H3k04me3StdHotspotsRep2 GM64 H3K4M3 Ht 2 H3K4me3 GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002038 2038 GSM945296 Stam UW DS18900 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneGm12864H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12864 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12864H3k04me3StdHotspotsRep1 GM64 H3K4M3 Ht 1 H3K4me3 GM12864 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH002038 2038 GSM945296 Stam UW DS18706 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneGm12864H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12864 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k36me3StdHotspotsRep2 GM90 H3K36M3 Ht 2 H3K36me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000444 444 GSM945213 Stam UW DS12189 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneGm06990H3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k36me3StdHotspotsRep1 GM90 H3K36M3 Ht 1 H3K36me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000444 444 GSM945213 Stam UW DS12192 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneGm06990H3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k27me3StdHotspotsRep2 GM90 H3K27M3 Ht 2 H3K27me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000427 427 GSM945205 Stam UW DS12188 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneGm06990H3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k27me3StdHotspotsRep1 GM90 H3K27M3 Ht 1 H3K27me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000427 427 GSM945205 Stam UW DS12191 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneGm06990H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k4me3StdHotspotsRep2 GM90 H3K4M3 Ht 2 H3K4me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-12 2010-07-11 wgEncodeEH000417 417 GSM945179 Stam UW DS11519 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneGm06990H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm06990H3k4me3StdHotspotsRep1 GM90 H3K4M3 Ht 1 H3K4me3 GM06990 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-13 2010-07-12 wgEncodeEH000417 417 GSM945179 Stam UW DS11521 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneGm06990H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM06990 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k36me3StdHotspotsRep2 Caco H3K36M3 Ht 2 H3K36me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000426 426 GSM945206 Stam UW DS12405 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneCaco2H3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k36me3StdHotspotsRep1 Caco H3K36M3 Ht 1 H3K36me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-19 2010-07-19 wgEncodeEH000426 426 GSM945206 Stam UW DS12406 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneCaco2H3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k27me3StdHotspotsRep2 Caco H3K27M3 Ht 2 H3K27me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000425 425 GSM945203 Stam UW DS12218 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneCaco2H3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k27me3StdHotspotsRep1 Caco H3K27M3 Ht 1 H3K27me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-10-20 2010-07-20 wgEncodeEH000425 425 GSM945203 Stam UW DS12221 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneCaco2H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k4me3StdHotspotsRep2 Caco H3K4M3 Ht 2 H3K4me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-09-29 2010-06-29 wgEncodeEH000407 407 GSM945162 Stam UW DS11785 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneCaco2H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCaco2H3k4me3StdHotspotsRep1 Caco H3K4M3 Ht 1 H3K4me3 Caco-2 std ChipSeq ENCODE June 2010 Freeze 2010-06-11 2009-09-29 2010-06-29 wgEncodeEH000407 407 GSM945162 Stam UW DS11784 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneCaco2H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. colorectal adenocarcinoma. (PMID: 1939345) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Caco-2 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k36me3StdHotspotsRep2 BJ H3K36M3 Ht 2 H3K36me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000443 443 GSM945207 Stam UW DS12195 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneBjH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k36me3StdHotspotsRep1 BJ H3K36M3 Ht 1 H3K36me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2010-06-10 2011-03-10 wgEncodeEH000443 443 GSM945207 Stam UW DS12198 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneBjH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k27me3StdHotspotsRep2 BJ H3K27M3 Ht 2 H3K27me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-20 2010-07-20 wgEncodeEH000424 424 GSM945204 Stam UW DS12197 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneBjH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k27me3StdHotspotsRep1 BJ H3K27M3 Ht 1 H3K27me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-19 2010-07-19 wgEncodeEH000424 424 GSM945204 Stam UW DS12194 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneBjH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k4me3StdHotspotsRep2 BJ H3K4M3 Ht 2 H3K4me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-12 2010-07-11 wgEncodeEH000416 416 GSM945178 Stam UW DS11561 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneBjH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBjH3k4me3StdHotspotsRep1 BJ H3K4M3 Ht 1 H3K4me3 BJ std ChipSeq ENCODE June 2010 Freeze 2010-06-10 2009-10-13 2010-07-12 wgEncodeEH000416 416 GSM945178 Stam UW DS11563 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneBjH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC. (PMID: 9916803) Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BJ H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cH3k04me3StdHotspotsRep2 BE2_C H3K4M3 Ht 2 H3K4me3 BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001906 1906 GSM945241 Stam UW DS18310 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneBe2cH3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BE2_C H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneBe2cH3k04me3StdHotspotsRep1 BE2_C H3K4M3 Ht 1 H3K4me3 BE2_C std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001906 1906 GSM945241 Stam UW DS18309 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneBe2cH3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm BE2_C H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafH3k4me3StdHotspotsRep2 AoAF H3K4M3 Ht 2 H3K4me3 AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000937 937 GSM945170 Stam UW DS15747 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneAoafH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AoAF H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAoafH3k4me3StdHotspotsRep1 AoAF H3K4M3 Ht 1 H3K4me3 AoAF std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000937 937 GSM945170 Stam UW DS15746 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneAoafH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. aortic adventitial fibroblast cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AoAF H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803H3k4me3StdHotspotsRep2 AG03 H3K4M3 Ht 2 H3K4me3 AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000935 935 GSM945172 Stam UW DS15745 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneAg10803H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG10803 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg10803H3k4me3StdHotspotsRep1 AG03 H3K4M3 Ht 1 H3K4me3 AG10803 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000935 935 GSM945172 Stam UW DS15744 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneAg10803H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG10803 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319H3k4me3StdHotspotsRep2 AG19 H3K4M3 Ht 2 H3K4me3 AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000933 933 GSM945166 Stam UW DS15743 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneAg09319H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09319 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09319H3k4me3StdHotspotsRep1 AG19 H3K4M3 Ht 1 H3K4me3 AG09319 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000933 933 GSM945166 Stam UW DS15742 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneAg09319H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. gum tissue fibroblasts from apparently heathly 24 year old Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09319 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309H3k4me3StdHotspotsRep2 AG09 H3K4M3 Ht 2 H3K4me3 AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000931 931 GSM945168 Stam UW DS16033 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneAg09309H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09309 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg09309H3k4me3StdHotspotsRep1 AG09 H3K4M3 Ht 1 H3K4me3 AG09309 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000931 931 GSM945168 Stam UW DS16034 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneAg09309H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG09309 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k27me3StdHotspotsRep1 AG50 H3K27m3 Ht 1 H3K27me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003036 3036 GSM1010913 Stam UW DS21480 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneAg04450H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k27acStdHotspotsRep1 AG50 H3K27ac Ht 1 H3K27ac AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003035 3035 GSM1010912 Stam UW DS21479 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneAg04450H3k27acStdHotspotsRep1 None Hotspots Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 H3K27ac Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k09me3StdHotspotsRep2 AG50 H3K9me3 Ht 2 H3K9me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003037 3037 GSM1010914 Stam UW DS21481 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneAg04450H3k09me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 H3K9me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k09me3StdHotspotsRep1 AG50 H3K9me3 Ht 1 H3K9me3 AG04450 std ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEH003037 3037 GSM1010914 Stam UW DS21482 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneAg04450H3k09me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 H3K9me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k4me3StdHotspotsRep2 AG50 H3K4M3 Ht 2 H3K4me3 AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000929 929 GSM945177 Stam UW DS15741 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneAg04450H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04450H3k4me3StdHotspotsRep1 AG50 H3K4M3 Ht 1 H3K4me3 AG04450 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000929 929 GSM945177 Stam UW DS15740 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneAg04450H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal lung fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04450 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449H3k4me3StdHotspotsRep2 AG49 H3K4M3 Ht 2 H3K4me3 AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000927 927 GSM945187 Stam UW DS15739 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneAg04449H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04449 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneAg04449H3k4me3StdHotspotsRep1 AG49 H3K4M3 Ht 1 H3K4me3 AG04449 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-22 2011-07-22 wgEncodeEH000927 927 GSM945187 Stam UW DS15737 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneAg04449H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. fetal buttock/thigh fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm AG04449 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746H3k27me3StdHotspotsRep1 CD14 H3K27M3 Ht 1 H3K27me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002167 2167 GSM945301 Stam UW DS19094 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneMonocd14ro1746H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Monocytes-CD14+ RO 01746 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMonocd14ro1746H3k04me3StdHotspotsRep1 CD14 H3K4M3 Ht 1 H3K4me3 Monocytes-CD14+_RO01746 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-21 2012-06-21 wgEncodeEH002168 2168 GSM945225 Stam UW DS18981 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneMonocd14ro1746H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Monocytes-CD14+ are CD14-positive cells from human leukapheresis production, from donor RO 01746 (draw 1 ID is RO 01746, draw 2 ID is RO 01826), Monocytes-CD14+_RO01746 and Monocytes-CD14+_RO01826 are being used as replicates, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm Monocytes-CD14+ RO 01746 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7H3k04me3StdHotspotsRep2 MCF7 H3K4M3 Ht 2 H3K4me3 MCF-7 std ChipSeq ENCODE Mar 2012 Freeze 2011-07-29 2012-04-28 wgEncodeEH000967 967 GSM945269 Stam UW DS16201 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneMcf7H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneMcf7H3k4me3StdHotspotsRep1 MCF7 H3K4M3 Ht 1 H3K4me3 MCF-7 std ChipSeq ENCODE Jan 2011 Freeze 2010-10-23 2011-07-23 wgEncodeEH000967 967 GSM945269 Stam UW DS16202 Hotspot-v5.1 hg19 1 exp wgEncodeUwHistoneMcf7H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm MCF-7 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k36me3StdHotspotsRep2 HUVE H3K36M3 Ht 2 H3K36me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000431 431 GSM945233 Stam UW DS12225 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHuvecH3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k36me3StdHotspotsRep1 HUVE H3K36M3 Ht 1 H3K36me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000431 431 GSM945233 Stam UW DS12228 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHuvecH3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k27me3StdHotspotsRep2 HUVE H3K27M3 Ht 2 H3K27me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-12 2010-07-12 wgEncodeEH000411 411 GSM945180 Stam UW DS12224 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHuvecH3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k27me3StdHotspotsRep1 HUVE H3K27M3 Ht 1 H3K27me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000411 411 GSM945180 Stam UW DS12227 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHuvecH3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k4me3StdHotspotsRep2 HUVE H3K4M3 Ht 2 H3K4me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-13 2010-07-12 wgEncodeEH000412 412 GSM945181 Stam UW DS11458 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHuvecH3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHuvecH3k4me3StdHotspotsRep1 HUVE H3K4M3 Ht 1 H3K4me3 HUVEC std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-09-29 2010-06-29 wgEncodeEH000412 412 GSM945181 Stam UW DS11460 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHuvecH3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. umbilical vein endothelial cells Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HUVEC H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k36me3StdHotspotsRep2 HepG H3K36M3 Ht 2 H3K36me3 HepG2 std ChipSeq ENCODE Jan 2011 Freeze 2010-07-24 2011-04-23 wgEncodeEH000446 446 GSM945211 Stam UW DS12075 Hotspot-v5.1 hg19 2 exp wgEncodeUwHistoneHepg2H3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k36me3StdHotspotsRep1 HepG H3K36M3 Ht 1 H3K36me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-14 wgEncodeEH000446 446 GSM945211 Stam UW DS12207 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHepg2H3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k27me3StdHotspotsRep2 HepG H3K27M3 Ht 2 H3K27me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000433 433 GSM945231 Stam UW DS12206 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHepg2H3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k27me3StdHotspotsRep1 HepG H3K27M3 Ht 1 H3K27me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000433 433 GSM945231 Stam UW DS12076 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHepg2H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k4me3StdHotspotsRep2 HepG H3K4M3 Ht 2 H3K4me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-09-29 2010-06-29 wgEncodeEH000413 413 GSM945182 Stam UW DS11780 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHepg2H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHepg2H3k4me3StdHotspotsRep1 HepG H3K4M3 Ht 1 H3K4me3 HepG2 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-09-29 2010-06-29 wgEncodeEH000413 413 GSM945182 Stam UW DS11781 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHepg2H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. hepatocellular carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HepG2 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k36me3StdHotspotsRep2 HeLa H3K36M3 Ht 2 H3K36me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000432 432 GSM945230 Stam UW DS12201 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHelas3H3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k36me3StdHotspotsRep1 HeLa H3K36M3 Ht 1 H3K36me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000432 432 GSM945230 Stam UW DS12071 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHelas3H3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k27me3StdHotspotsRep2 HeLa H3K27M3 Ht 2 H3K27me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000442 442 GSM945208 Stam UW DS12070 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHelas3H3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k27me3StdHotspotsRep1 HeLa H3K27M3 Ht 1 H3K27me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000442 442 GSM945208 Stam UW DS12072 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHelas3H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k4me3StdHotspotsRep2 HeLa H3K4M3 Ht 2 H3K4me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-13 2010-07-12 wgEncodeEH000423 423 GSM945201 Stam UW DS11553 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneHelas3H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneHelas3H3k4me3StdHotspotsRep1 HeLa H3K4M3 Ht 1 H3K4me3 HeLa-S3 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-13 2010-07-12 wgEncodeEH000423 423 GSM945201 Stam UW DS11555 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneHelas3H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. cervical carcinoma Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm HeLa-S3 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01794H3k04me3StdHotspotsRep3 20+94 H3K4M3 Ht 3 H3K4me3 CD20+_RO01794 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEH002171 2171 GSM945198 Stam UW DS18983 Hotspot-v5.2 hg19 3 exp wgEncodeUwHistoneCd20ro01794H3k04me3StdHotspotsRep3 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, African American, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm CD20+ (RO 01794) H3K4me3 Histone Mod ChIP-seq Hotspots 3 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778H3k04me3StdHotspotsRep2 20+78 H3K4M3 Ht 2 H3K4me3 CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2012-06-08 wgEncodeEH002166 2166 GSM945229 Stam UW DS18986 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneCd20ro01778H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm CD20+ (RO 01778) H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneCd20ro01778H3k04me3StdHotspotsRep1 20+78 H3K4M3 Ht 1 H3K4me3 CD20+_RO01778 std ChipSeq ENCODE Mar 2012 Freeze 2011-09-14 2012-06-14 wgEncodeEH002166 2166 GSM945229 Stam UW DS18985 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneCd20ro01778H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B cells, caucasian, draw number 1, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm CD20+ (RO 01778) H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549H3k04me3StdHotspotsRep2 A549 H3K4M3 Ht 2 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001905 1905 GSM945244 Stam UW DS18304 Hotspot-v5.2 hg19 2 exp wgEncodeUwHistoneA549H3k04me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm A549 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneA549H3k04me3StdHotspotsRep1 A549 H3K4M3 Ht 1 H3K4me3 A549 std ChipSeq ENCODE Mar 2012 Freeze 2011-06-25 2012-03-24 wgEncodeEH001905 1905 GSM945244 Stam UW DS18305 Hotspot-v5.2 hg19 1 exp wgEncodeUwHistoneA549H3k04me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. epithelial cell line derived from a lung carcinoma tissue. (PMID: 175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2: not in 2011 analysis Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm A549 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k36me3StdHotspotsRep2 K562 H3K36M3 Ht 2 H3K36me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000435 435 GSM945302 Stam UW DS12177 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneK562H3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k36me3StdHotspotsRep1 K562 H3K36M3 Ht 1 H3K36me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000435 435 GSM945302 Stam UW DS12067 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneK562H3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k27me3StdHotspotsRep2 K562 H3K27M3 Ht 2 H3K27me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000434 434 GSM945228 Stam UW DS12068 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneK562H3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k27me3StdHotspotsRep1 K562 H3K27M3 Ht 1 H3K27me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-10-19 2010-07-19 wgEncodeEH000434 434 GSM945228 Stam UW DS12066 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneK562H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k4me3StdHotspotsRep2 K562 H3K4M3 Ht 2 H3K4me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2010-06-15 2011-03-15 wgEncodeEH000400 400 GSM945165 Stam UW DS11509 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneK562H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneK562H3k4me3StdHotspotsRep1 K562 H3K4M3 Ht 1 H3K4me3 K562 std ChipSeq ENCODE June 2010 Freeze 2010-06-15 2009-06-30 2010-03-29 wgEncodeEH000400 400 GSM945165 Stam UW DS11507 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneK562H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm K562 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k36me3StdHotspotsRep2 GM78 H3K36M3 Ht 2 H3K36me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000445 445 GSM945212 Stam UW DS12183 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneGm12878H3k36me3StdHotspotsRep2 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 H3K36me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k36me3StdHotspotsRep1 GM78 H3K36M3 Ht 1 H3K36me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2010-06-14 2011-03-14 wgEncodeEH000445 445 GSM945212 Stam UW DS12186 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneGm12878H3k36me3StdHotspotsRep1 None Hotspots Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 H3K36me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k27me3StdHotspotsRep2 GM78 H3K27M3 Ht 2 H3K27me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-20 2010-07-20 wgEncodeEH000428 428 GSM945196 Stam UW DS12185 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneGm12878H3k27me3StdHotspotsRep2 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 H3K27me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k27me3StdHotspotsRep1 GM78 H3K27M3 Ht 1 H3K27me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-19 2010-07-19 wgEncodeEH000428 428 GSM945196 Stam UW DS12182 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneGm12878H3k27me3StdHotspotsRep1 None Hotspots Histone H3 (tri-methyl K27). Marks promoters that are silenced by Polycomb proteins in a given lineage; large domains are found at inactive developmental loci. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 H3K27me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k4me3StdHotspotsRep2 GM78 H3K4M3 Ht 2 H3K4me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-10-12 2010-07-11 wgEncodeEH000395 395 GSM945188 Stam UW DS11511 Hotspot-v5.1 hg18 2 exp wgEncodeUwHistoneGm12878H3k4me3StdHotspotsRep2 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 H3K4me3 Histone Mod ChIP-seq Hotspots 2 from ENCODE/UW Regulation 
wgEncodeUwHistoneGm12878H3k4me3StdHotspotsRep1 GM78 H3K4M3 Ht 1 H3K4me3 GM12878 std ChipSeq ENCODE June 2010 Freeze 2010-06-14 2009-06-30 2010-03-29 wgEncodeEH000395 395 GSM945188 Stam UW DS11513 Hotspot-v5.1 hg18 1 exp wgEncodeUwHistoneGm12878H3k4me3StdHotspotsRep1 None Hotspots Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus Standard input signal for most experiments. Chromatin IP Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington ChIP-seq affinity zones identified using the HotSpot algorithm GM12878 H3K4me3 Histone Mod ChIP-seq Hotspots 1 from ENCODE/UW Regulation 
dbSnp153Composite dbSNP 153 Short Genetic Variants from dbSNP release 153 Variation Description This track shows short genetic variants (up to approximately 50 base pairs) from dbSNP build 153: single-nucleotide variants (SNVs), small insertions, deletions, and complex deletion/insertions (indels), relative to the reference genome assembly. Most variants in dbSNP are rare, not true polymorphisms, and some variants are known to be pathogenic. For hg38 (GRCh38), approximately 667 million distinct variants (RefSNP clusters with rs# ids) have been mapped to more than 702 million genomic locations including alternate haplotype and fix patch sequences. dbSNP remapped variants from hg38 to hg19 (GRCh37); approximately 658 million distinct variants were mapped to more than 683 million genomic locations including alternate haplotype and fix patch sequences (not all of which are included in UCSC's hg19). This track includes four subtracks of variants: All dbSNP (153): the entire set (683 million for hg19, 702 million for hg38) Common dbSNP (153): approximately 15 million variants with a minor allele frequency (MAF) of at least 1% (0.01) in the 1000 Genomes Phase 3 dataset. Variants in the Mult. subset (below) are excluded. ClinVar dbSNP (153): approximately 455,000 variants mentioned in ClinVar. Note: that includes both benign and pathogenic (as well as uncertain) variants. Variants in the Mult. subset (below) are excluded. Mult. dbSNP (153): variants that have been mapped to multiple chromosomes, for example chr1 and chr2, raising the question of whether the variant is really a variant or just a difference between duplicated sequences. There are some exceptions in which a variant is mapped to more than one reference sequence, but not culled into this set: A variant may appear in both X and Y pseudo-autosomal regions (PARs) without being included in this set. A variant may also appear in a main chromosome as well as an alternate haplotype or fix patch sequence assigned to that chromosome. A fifth subtrack highlights coordinate ranges to which dbSNP mapped a variant but with genomic coordinates that are not internally consistent, i.e. different coordinate ranges were provided when describing different alleles. This can occur due to a bug with mapping variants from one assembly sequence to another when there is an indel difference between the assembly sequences: Map Err (153): around 120,000 mappings of 55,000 distinct rsIDs for hg19 and 149,000 mappings of 86,000 distinct rsIDs for hg38. Interpreting and Configuring the Graphical Display SNVs and pure deletions are displayed as boxes covering the affected base(s). Pure insertions are drawn as single-pixel tickmarks between the base before and the base after the insertion. Insertions and/or deletions in repetitive regions may be represented by a half-height box showing uncertainty in placement, followed by a full-height box showing the number of deleted bases, or a full-height tickmark to indicate an insertion. When an insertion or deletion falls in a repetitive region, the placement may be ambiguous. For example, if the reference genome contains "TAAAG" but some individuals have "TAAG" at the same location, then the variant is a deletion of a single A relative to the reference genome. However, which A was deleted? There is no way to tell whether the first, second or third A was removed. Different variant mapping tools may place the deletion at different bases in the reference genome. To reduce errors in merging variant calls made with different left vs. right biases, dbSNP made a major change in its representation of deletion/insertion variants in build 152. Now, instead of assigning a single-base genomic location at one of the A's, dbSNP expands the coordinates to encompass the whole repetitive region, so the variant is represented as a deletion of 3 A's combined with an insertion of 2 A's. In the track display, there will be a half-height box covering the first two A's, followed by a full-height box covering the third A, to show a net loss of one base but an uncertain placement within the three A's. Variants are colored according to functional effect on genes annotated by dbSNP: Protein-altering variants and splice site variants are red. Synonymous codon variants are green. Non-coding transcript or Untranslated Region (UTR) variants are blue. On the track controls page, several variant properties can be included or excluded from the item labels: rs# identifier assigned by dbSNP, reference/alternate alleles, major/minor alleles (when available) and minor allele frequency (when available). Allele frequencies are reported independently by twelve projects (some of which may have overlapping sets of samples): 1000Genomes: The 1000 Genomes Phase 3 dataset contains data for 2,504 individuals from 26 populations. GnomAD exomes: The gnomAD v2.1 exome dataset comprises a total of 16 million SNVs and 1.2 million indels from 125,748 exomes in 14 populations. TOPMED: The TOPMED dataset contains phase 3 data from freeze 5 panel that include more than 60,000 individuals. The approximate ethnic breakdown is European(52%), African (31%), Hispanic or Latino (10%), and East Asian (7%) ancestry. PAGE STUDY: The PAGE Study: How Genetic Diversity Improves Our Understanding of the Architecture of Complex Traits. GnomAD genomes: The gnomAD v2.1 genome dataset includes 229 million SNVs and 33 million indels from 15,708 genomes in 9 populations. GoESP: The NHLBI Grand Opportunity Exome Sequencing Project (GO-ESP) dataset contains 6503 samples drawn from multiple ESP cohorts and represents all of the ESP exome variant data. Estonian: Genetic variation in the Estonian population: pharmacogenomics study of adverse drug effects using electronic health records. ALSPAC: The UK10K - Avon Longitudinal Study of Parents and Children project contains 1927 sample including individuals obtained from the ALSPAC population. This population contains more than 14,000 mothers enrolled during pregnancy in 1991 and 1992. TWINSUK: The UK10K - TwinsUK project contains 1854 samples from the Department of Twin Research and Genetic Epidemiology (DTR). The DTR dataset contains data obtained from the 11,000 identical and non-identical twins between the ages of 16 and 85 years old. NorthernSweden: Whole-genome sequenced control population in northern Sweden reveals subregional genetic differences. This population consists of 300 whole genome sequenced human samples selected from the county of Vasterbotten in northern Sweden. To be selected for inclusion into the population, the individuals had to have reached at least 80 years of age and have no diagnosed cancer. Vietnamese: The Vietnamese Genetic Variation Database includes about 25 million variants (SNVs and indels) from 406 genomes and 305 exomes of unrelated healthy Kinh Vietnamese (KHV) people. The project from which to take allele frequency data defaults to 1000 Genomes but can be set to any of those projects. Using the track controls, variants can be filtered by minimum minor allele frequency (MAF) variation class/type (e.g. SNV, insertion, deletion) functional effect on a gene (e.g. synonymous, frameshift, intron, upstream) assorted features and anomalies noted by UCSC during processing of dbSNP's data Interesting and anomalous conditions noted by UCSC While processing the information downloaded from dbSNP, UCSC annotates some properties of interest. These are noted on the item details page, and may be useful to include or exclude affected variants. Some are purely informational: keyword in data file (dbSnp153.bb) # in hg19# in hg38description clinvar 454678 453996 Variant is in ClinVar. clinvarBenign 143864 143736 Variant is in ClinVar with clinical significance of benign and/or likely benign. clinvarConflicting 7932 7950 Variant is in ClinVar with reports of both benign and pathogenic significance. clinvarPathogenic 96242 95262 Variant is in ClinVar with clinical significance of pathogenic and/or likely pathogenic. commonAll 12184521 12438655 Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in all projects reporting frequencies. commonSome 20541190 20902944 Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in some, but not all, projects reporting frequencies. diffMajor 1377831 1399109 Different frequency sources have different major alleles. overlapDiffClass 107015341 110007682 This variant overlaps another variant with a different type/class. overlapSameClass 16915239 17291289 This variant overlaps another with the same type/class but different start/end. rareAll 662601770 681696398 Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% in all projects reporting frequencies, or has no frequency data. rareSome 670958439 690160687 Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% in some, but not all, projects reporting frequencies, or has no frequency data. revStrand 3813702 4532511 Alleles are displayed on the + strand at the current position. dbSNP's alleles are displayed on the + strand of a different assembly sequence, so dbSNP's variant page shows alleles that are reverse-complemented with respect to the alleles displayed above. while others may indicate that the reference genome contains a rare variant or sequencing issue: keyword in data file (dbSnp153.bb) # in hg19# in hg38description refIsAmbiguous 101 111 The reference genome allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G', or 'N' for 'any base'). refIsMinor 3272116 3360435 The reference genome allele is not the major allele in at least one project. refIsRare 136547 160827 The reference genome allele is rare (i.e. allele frequency refIsSingleton 37832 50927 The reference genome allele has never been observed in a population sequencing project reporting frequencies. refMismatch 4 33 The reference genome allele reported by dbSNP differs from the GenBank assembly sequence. This is very rare and in all cases observed so far, the GenBank assembly has an 'N' while the RefSeq assembly used by dbSNP has a less ambiguous character such as 'R'. and others may indicate an anomaly or problem with the variant data: keyword in data file (dbSnp153.bb) # in hg19# in hg38description altIsAmbiguous 10755 10888 At least one alternate allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G'). For alleles containing more than one ambiguous base, this may create a combinatoric explosion of possible alleles. classMismatch 5998 6216 Variation class/type is inconsistent with alleles mapped to this genome assembly. clusterError 114826 128306 This variant has the same start, end and class as another variant; they probably should have been merged into one variant. freqIncomplete 3922 4673 At least one project reported counts for only one allele which implies that at least one allele is missing from the report; that project's frequency data are ignored. freqIsAmbiguous 7656 7756 At least one allele reported by at least one project that reports frequencies contains an IUPAC ambiguous base. freqNotMapped 2685 6590 At least one project reported allele frequencies relative to a different assembly; However, dbSNP does not include a mapping of this variant to that assembly, which implies a problem with mapping the variant across assemblies. The mapping on this assembly may have an issue; evaluate carefully vs. original submissions, which you can view by clicking through to dbSNP above. freqNotRefAlt 17694 32170 At least one allele reported by at least one project that reports frequencies does not match any of the reference or alternate alleles listed by dbSNP. multiMap 562180 132123 This variant has been mapped to more than one distinct genomic location. otherMapErr 114095 204219 At least one other mapping of this variant has erroneous coordinates. The mapping(s) with erroneous coordinates are excluded from this track and are included in the Map Err subtrack. Sometimes despite this mapping having legal coordinates, there may still be an issue with this mapping's coordinates and alleles; you may want to click through to dbSNP to compare the initial submission's coordinates and alleles. In hg19, 55454 distinct rsIDs are affected; in hg38, 86636. Data Sources and Methods dbSNP has collected genetic variant reports from researchers worldwide for more than 20 years. Since the advent of next-generation sequencing methods and the population sequencing efforts that they enable, dbSNP has grown exponentially, requiring a new data schema, computational pipeline, web infrastructure, and download files. (Holmes et al.) The same challenges of exponential growth affected UCSC's presentation of dbSNP variants, so we have taken the opportunity to change our internal representation and import pipeline. Most notably, flanking sequences are no longer provided by dbSNP, because most submissions have been genomic variant calls in VCF format as opposed to independent sequences. We downloaded JSON files available from dbSNP at ftp://ftp.ncbi.nlm.nih.gov/snp/archive/b153/JSON/, extracted a subset of the information about each variant, and collated it into a bigBed file using the bigDbSnp.as schema with the information necessary for filtering and displaying the variants, as well as a separate file containing more detailed information to be displayed on each variant's details page (dbSnpDetails.as schema). Data Access Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry. Since dbSNP has grown to include approximately 700 million variants, the size of the All dbSNP (153) subtrack can cause the Table Browser and Data Integrator to time out, leading to a blank page or truncated output, unless queries are restricted to a chromosomal region, to particular defined regions, to a specific set of rs# IDs (which can be pasted/uploaded into the Table Browser), or to one of the subset tracks such as Common (~15 million variants) or ClinVar (~0.5M variants). For automated analysis, the track data files can be downloaded from the downloads server for hg19 and hg38. file format subtrack dbSnp153.bb hg19 hg38 bigDbSnp (bigBed4+13) All dbSNP (153) dbSnp153ClinVar.bb hg19 hg38 bigDbSnp (bigBed4+13) ClinVar dbSNP (153) dbSnp153Common.bb hg19 hg38 bigDbSnp (bigBed4+13) Common dbSNP (153) dbSnp153Mult.bb hg19 hg38 bigDbSnp (bigBed4+13) Mult. dbSNP (153) dbSnp153BadCoords.bb hg19 hg38 bigBed4 Map Err (153) dbSnp153Details.tab.gz gzip-compressed tab-separated text Detailed variant properties, independent of genome assembly version Several utilities for working with bigBed-formatted binary files can be downloaded here. Run a utility with no arguments to see a brief description of the utility and its options. bigBedInfo provides summary statistics about a bigBed file including the number of items in the file. With the -as option, the output includes an autoSql definition of data columns, useful for interpreting the column values. bigBedToBed converts the binary bigBed data to tab-separated text. Output can be restricted to a particular region by using the -chrom, -start and -end options. bigBedNamedItems extracts rows for one or more rs# IDs. Example: retrieve all variants in the region chr1:200001-200400 bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp153.bb -chrom=chr1 -start=200000 -end=200400 stdout Example: retrieve variant rs6657048 bigBedNamedItems dbSnp153.bb rs6657048 stdout Example: retrieve all variants with rs# IDs in file myIds.txt bigBedNamedItems -nameFile dbSnp153.bb myIds.txt dbSnp153.myIds.bed The columns in the bigDbSnp/bigBed files and dbSnp153Details.tab.gz file are described in bigDbSnp.as and dbSnpDetails.as respectively. For columns that contain lists of allele frequency data, the order of projects providing the data listed is as follows: 1000Genomes GnomAD exomes TOPMED PAGE STUDY GnomAD genomes GoESP Estonian ALSPAC TWINSUK NorthernSweden Vietnamese UCSC also has an API that can be used to retrieve values from a particular chromosome range. A list of rs# IDs can be pasted/uploaded in the Variant Annotation Integrator tool to find out which genes (if any) the variants are located in, as well as functional effect such as intron, coding-synonymous, missense, frameshift, etc. Please refer to our searchable mailing list archives for more questions and example queries, or our Data Access FAQ for more information. References Holmes JB, Moyer E, Phan L, Maglott D, Kattman B. SPDI: Data Model for Variants and Applications at NCBI. Bioinformatics. 2019 Nov 18;. PMID: 31738401 Sayers EW, Agarwala R, Bolton EE, Brister JR, Canese K, Clark K, Connor R, Fiorini N, Funk K, Hefferon T et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2019 Jan 8;47(D1):D23-D28. PMID: 30395293; PMC: PMC6323993 Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
dbSnpArchive dbSNP Archive dbSNP Track Archive Variation Description This composite track contains information about single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP, available from ftp.ncbi.nih.gov/snp. You can click into each track for a version/subset-specific description. This collection includes numbered versions of the entire dbSNP datasets (All SNP) as well as three tracks with subsets of the items in that version. Here is information on each of the subsets: dbSNP 153: The dbSNP build 153 is composed of 5 subtracks. Click the track for a description of the subtracks. Common SNPs: SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs: SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs: SNPs that have been mapped to multiple locations in the reference genome assembly. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF >= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF >= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/database/ (for human, organism_tax_id = human_9606; for mouse, organism_tax_id = mouse_10090). The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/ organism_tax_id/rs_fasta/ Coordinates, orientation, location type and dbSNP reference allele data were obtained from files like b138_SNPContigLoc.bcp.gz and b138_ContigInfo.bcp.gz. b138_SNPMapInfo.bcp.gz provides the alignment weights. Functional classification was obtained from files like b138_SNPContigLocusId.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry. The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation files can be downloaded in their entirety for hg38, hg19, and mm10 as (snp*.txt.gz). You can also make queries using the UCSC Genome Browser JSON API or public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download in the genome's snp*Mask folder. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exlcude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
dbSnp153ViewVariants Variants Short Genetic Variants from dbSNP release 153 Variation 
dbSnp153 All dbSNP(153) All Short Genetic Variants from dbSNP Release 153 Variation 
dbSnp153Mult dbSNP(153) Mult. Short Genetic Variants from dbSNP Release 153 that Map to Multiple Genomic Loci Variation 
dbSnp153ClinVar dbSNP(153) in ClinVar Short Genetic Variants from dbSNP Release 153 Included in ClinVar Variation 
dbSnp153Common Common dbSNP(153) Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 153 Variation 
dbSnp153ViewErrs Mapping Errors Short Genetic Variants from dbSNP release 153 Variation 
dbSnp153BadCoords Map Err dbSnp(153) Mappings with Inconsistent Coordinates from dbSNP 153 Variation 
snp151Common Common SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 151, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs that have a minor allele frequency (MAF) of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. Allele counts from all submissions that include frequency data are combined when determining MAF, so for example the allele counts from the 1000 Genomes Project and an independent submitter may be combined for the same variant. dbSNP provides download files in the Variant Call Format (VCF) that include a "COMMON" flag in the INFO column. That is determined by a different method, and is generally a superset of the UCSC Common set. dbSNP uses frequency data from the 1000 Genomes Project only, and considers a variant COMMON if it has a MAF of at least 0.01 in any of the five super-populations: African (AFR) Admixed American (AMR) East Asian (EAS) European (EUR) South Asian (SAS) In build 151, dbSNP marks approximately 38M variants as COMMON; 23M of those have a global MAF &lt; 0.01. The remainder should be in agreement with UCSC's Common subset. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(151) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(151) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(151) - SNPs mapping in more than one place on reference assembly. All SNPs(151) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b151_SNPContigLoc_N.bcp.gz and b151_ContigInfo_N.bcp.gz. (N = 105 for hg19, 108 for hg38) b151_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b151_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp151*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp151 All SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 151, available from ftp.ncbi.nlm.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(151): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(151): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(151): SNPs that have been mapped to multiple locations in the reference genome assembly. There are very few SNPs in this category because dbSNP has been filtering out almost all multiple-mapping SNPs since build 149. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(151) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(151) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(151) - SNPs mapping in more than one place on reference assembly. All SNPs(151) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b151_SNPContigLoc_N.bcp.gz and b151_ContigInfo_N.bcp.gz. (N = 105 for hg19, 108 for hg38) b151_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b151_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp151*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp151Flagged Flagged SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 151, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(151) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(151) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(151) - SNPs mapping in more than one place on reference assembly. All SNPs(151) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b151_SNPContigLoc_N.bcp.gz and b151_ContigInfo_N.bcp.gz. (N = 105 for hg19, 108 for hg38) b151_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b151_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp151*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp151Mult Mult. SNPs(151) Simple Nucleotide Polymorphisms (dbSNP 151) That Map to Multiple Genomic Loci Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 151, available from ftp.ncbi.nlm.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(151): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(151): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(151): SNPs that have been mapped to multiple locations in the reference genome assembly. There are very few SNPs in this category because dbSNP has been filtering out almost all multiple-mapping SNPs since build 149. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(151) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(151) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(151) - SNPs mapping in more than one place on reference assembly. All SNPs(151) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b151_SNPContigLoc_N.bcp.gz and b151_ContigInfo_N.bcp.gz. (N = 105 for hg19, 108 for hg38) b151_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b151_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp151*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp150 All SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 150, available from ftp.ncbi.nlm.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(150): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(150): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(150): SNPs that have been mapped to multiple locations in the reference genome assembly. There are very few SNPs in this category because dbSNP has been filtering out almost all multiple-mapping SNPs since build 149. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(150) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(150) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly. All SNPs(150) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b150_SNPContigLoc_N.bcp.gz and b150_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b150_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b150_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp150*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp150Common Common SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 150, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs that have a minor allele frequency (MAF) of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. Allele counts from all submissions that include frequency data are combined when determining MAF, so for example the allele counts from the 1000 Genomes Project and an independent submitter may be combined for the same variant. dbSNP provides download files in the Variant Call Format (VCF) that include a "COMMON" flag in the INFO column. That is determined by a different method, and is generally a superset of the UCSC Common set. dbSNP uses frequency data from the 1000 Genomes Project only, and considers a variant COMMON if it has a MAF of at least 0.01 in any of the five super-populations: African (AFR) Admixed American (AMR) East Asian (EAS) European (EUR) South Asian (SAS) In build 151 (which has replaced build 150 on the dbSNP web and download site), dbSNP marks approximately 38M variants as COMMON; 23M of those have a global MAF &lt; 0.01. The remainder should be in agreement with UCSC's Common subset. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(150) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(150) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly. All SNPs(150) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b150_SNPContigLoc_N.bcp.gz and b150_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b150_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b150_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp150*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp150Flagged Flagged SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 150, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(150) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(150) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly. All SNPs(150) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b150_SNPContigLoc_N.bcp.gz and b150_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b150_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b150_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp150*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp150Mult Mult. SNPs(150) Simple Nucleotide Polymorphisms (dbSNP 150) That Map to Multiple Genomic Loci Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 150, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs that have been mapped to multiple locations in the reference genome assembly are included in this subset. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. Since build 149, dbSNP has been filtering out almost all such "SNPs" so there are very few items in this track. The default maximum weight for this track is 3, unlike the other dbSNP build 150 tracks which have a maximum weight of 1. That enables these multiply-mapped SNPs to appear in the display, while by default they will not appear in the All SNPs(150) track because of its maximum weight filter. The remainder of this page is identical on the following tracks: Common SNPs(150) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(150) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(150) - SNPs mapping in more than one place on reference assembly. All SNPs(150) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors. If a SNP has more than one of these attributes, the stronger color will override the weaker color. The order of colors, from strongest to weakest, is red, green, blue, gray, and black. Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/database/data/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/database/data/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b150_SNPContigLoc_N.bcp.gz and b150_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b150_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b150_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp150*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp147 All SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 147, available from ftp.ncbi.nlm.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(147): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(147): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(147): SNPs that have been mapped to multiple locations in the reference genome assembly. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(147) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(147) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(147) - SNPs mapping in more than one place on reference assembly. All SNPs(147) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are always colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b147_SNPContigLoc_N.bcp.gz and b147_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b147_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b147_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp147*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp147Common Common SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 147, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(147) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(147) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(147) - SNPs mapping in more than one place on reference assembly. All SNPs(147) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are always colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b147_SNPContigLoc_N.bcp.gz and b147_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b147_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b147_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp147*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp147Flagged Flagged SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 147, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(147) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(147) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(147) - SNPs mapping in more than one place on reference assembly. All SNPs(147) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are always colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b147_SNPContigLoc_N.bcp.gz and b147_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b147_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b147_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp147*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp147Mult Mult. SNPs(147) Simple Nucleotide Polymorphisms (dbSNP 147) That Map to Multiple Genomic Loci Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 147, available from ftp.ncbi.nlm.nih.gov/snp. Only SNPs that have been mapped to multiple locations in the reference genome assembly are included in this subset. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The default maximum weight for this track is 3, unlike the other dbSNP build 147 tracks which have a maximum weight of 1. That enables these multiply-mapped SNPs to appear in the display, while by default they will not appear in the All SNPs(147) track because of its maximum weight filter. The remainder of this page is identical on the following tracks: Common SNPs(147) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(147) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as &quot;clinically associated&quot; -- not necessarily a risk allele! Mult. SNPs(147) - SNPs mapping in more than one place on reference assembly. All SNPs(147) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Non-coding (ncRNA): (nc_transcript_variant) are always colored blue. Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP. Before dbSNP build 147, weight had values 1, 2 or 3, with 1 being the highest quality (mapped to a single genomic location). As of dbSNP build 147, dbSNP now releases only the variants with weight 1. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a &quot;|&quot; indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period &gt;= 12) is shown in lower case, and matching bases are indicated by a &quot;+&quot;. Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b147_SNPContigLoc_N.bcp.gz and b147_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b147_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b147_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp147*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp146 All SNPs(146) Simple Nucleotide Polymorphisms (dbSNP 146) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 146, available from ftp.ncbi.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(146): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(146): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(146): SNPs that have been mapped to multiple locations in the reference genome assembly. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(146) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(146) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(146) - SNPs mapping in more than one place on reference assembly. All SNPs(146) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b146_SNPContigLoc_N.bcp.gz and b146_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b146_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b146_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp146*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp146Common Common SNPs(146) Simple Nucleotide Polymorphisms (dbSNP 146) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 146, available from ftp.ncbi.nih.gov/snp. Only SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(146) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(146) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(146) - SNPs mapping in more than one place on reference assembly. All SNPs(146) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b146_SNPContigLoc_N.bcp.gz and b146_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b146_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b146_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp146*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp146Flagged Flagged SNPs(146) Simple Nucleotide Polymorphisms (dbSNP 146) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 146, available from ftp.ncbi.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(146) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(146) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(146) - SNPs mapping in more than one place on reference assembly. All SNPs(146) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b146_SNPContigLoc_N.bcp.gz and b146_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b146_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b146_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp146*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp146Mult Mult. SNPs(146) Simple Nucleotide Polymorphisms (dbSNP 146) That Map to Multiple Genomic Loci Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 146, available from ftp.ncbi.nih.gov/snp. Only SNPs that have been mapped to multiple locations in the reference genome assembly are included in this subset. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The default maximum weight for this track is 3, unlike the other dbSNP build 146 tracks which have a maximum weight of 1. That enables these multiply-mapped SNPs to appear in the display, while by default they will not appear in the All SNPs(146) track because of its maximum weight filter. The remainder of this page is identical on the following tracks: Common SNPs(146) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(146) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(146) - SNPs mapping in more than one place on reference assembly. All SNPs(146) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b146_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b146_SNPContigLoc_N.bcp.gz and b146_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b146_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b146_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp146*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp144 All SNPs(144) Simple Nucleotide Polymorphisms (dbSNP 144) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 144, available from ftp.ncbi.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(144): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(144): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(144): SNPs that have been mapped to multiple locations in the reference genome assembly. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(144) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(144) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(144) - SNPs mapping in more than one place on reference assembly. All SNPs(144) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b144_SNPContigLoc_N.bcp.gz and b144_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b144_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b144_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp144*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp144Common Common SNPs(144) Simple Nucleotide Polymorphisms (dbSNP 144) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 144, available from ftp.ncbi.nih.gov/snp. Only SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(144) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(144) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(144) - SNPs mapping in more than one place on reference assembly. All SNPs(144) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b144_SNPContigLoc_N.bcp.gz and b144_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b144_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b144_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp144*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp144Flagged Flagged SNPs(144) Simple Nucleotide Polymorphisms (dbSNP 144) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 144, available from ftp.ncbi.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(144) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(144) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(144) - SNPs mapping in more than one place on reference assembly. All SNPs(144) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b144_SNPContigLoc_N.bcp.gz and b144_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b144_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b144_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp144*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp144Mult Mult. SNPs(144) Simple Nucleotide Polymorphisms (dbSNP 144) That Map to Multiple Genomic Loci Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 144, available from ftp.ncbi.nih.gov/snp. Only SNPs that have been mapped to multiple locations in the reference genome assembly are included in this subset. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The default maximum weight for this track is 3, unlike the other dbSNP build 144 tracks which have a maximum weight of 1. That enables these multiply-mapped SNPs to appear in the display, while by default they will not appear in the All SNPs(144) track because of its maximum weight filter. The remainder of this page is identical on the following tracks: Common SNPs(144) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(144) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(144) - SNPs mapping in more than one place on reference assembly. All SNPs(144) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b144_GRCh38p2/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b144_SNPContigLoc_N.bcp.gz and b144_ContigInfo_N.bcp.gz. (N = 105 for hg19, 107 for hg38) b144_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b144_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp144*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp142 All SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142) Variation Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 142, available from ftp.ncbi.nih.gov/snp. Three tracks contain subsets of the items in this track: Common SNPs(142): SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly. Frequency data are not available for all SNPs, so this subset is incomplete. Flagged SNPs(142): SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%. Frequency data are not available for all SNPs, so this subset may include some SNPs whose true minor allele frequency is 1% or greater. Mult. SNPs(142): SNPs that have been mapped to multiple locations in the reference genome assembly. The default maximum weight for this track is 1, so unless the setting is changed in the track controls, SNPs that map to multiple genomic locations will be omitted from display. When a SNP's flanking sequences map to multiple locations in the reference genome, it calls into question whether there is true variation at those sites, or whether the sequences at those sites are merely highly similar but not identical. The remainder of this page is identical on the following tracks: Common SNPs(142) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(142) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(142) - SNPs mapping in more than one place on reference assembly. All SNPs(142) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b142_SNPContigLoc_N.bcp.gz and b142_ContigInfo_N.bcp.gz. (N = 105 for hg19, 106 for hg38) b142_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b142_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp142*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp142Common Common SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 142, available from ftp.ncbi.nih.gov/snp. Only SNPs that have a minor allele frequency of at least 1% and are mapped to a single location in the reference genome assembly are included in this subset. Frequency data are not available for all SNPs, so this subset is incomplete. The selection of SNPs with a minor allele frequency of 1% or greater is an attempt to identify variants that appear to be reasonably common in the general population. Taken as a set, common variants should be less likely to be associated with severe genetic diseases due to the effects of natural selection, following the view that deleterious variants are not likely to become common in the population. However, the significance of any particular variant should be interpreted only by a trained medical geneticist using all available information. The remainder of this page is identical on the following tracks: Common SNPs(142) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(142) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(142) - SNPs mapping in more than one place on reference assembly. All SNPs(142) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's submitters studied this SNP in a biomedical setting, but is not a Locus-Specific Database or OMIM/OMIA. Submitted by Locus-Specific Database - At least one of the SNP's submitters is associated with a database of variants associated with a particular gene. These variants may or may not be known to be causative. MAF &gt;= 5% in Some Population - Minor Allele Frequency is at least 5% in at least one population assayed. MAF &gt;= 5% in All Populations - Minor Allele Frequency is at least 5% in all populations assayed. Genotype Conflict - Quality check: different genotypes have been submitted for the same individual. Ref SNP Cluster has Non-overlapping Alleles - Quality check: this reference SNP was clustered from submitted SNPs with non-overlapping sets of observed alleles. Some Assembly's Allele Does Not Match Observed - Quality check: at least one assembly mapped by dbSNP has an allele at the mapped position that is not present in this SNP's observed alleles. Several other properties do not have coloring options, but do have some filtering options: Average heterozygosity: Calculated by dbSNP as described in Computation of Average Heterozygosity and Standard Error for dbSNP RefSNP Clusters. Average heterozygosity should not exceed 0.5 for bi-allelic single-base substitutions. Weight: Alignment quality assigned by dbSNP Weight can be 0, 1, 2, 3 or 10. Weight = 1 are the highest quality alignments. Weight = 0 and weight = 10 are excluded from the data set. A filter on maximum weight value is supported, which defaults to 1 on all tracks except the Mult. SNPs track, which defaults to 3. Submitter handles: These are short, single-word identifiers of labs or consortia that submitted SNPs that were clustered into this reference SNP by dbSNP (e.g., 1000GENOMES, ENSEMBL, KWOK). Some SNPs have been observed by many different submitters, and some by only a single submitter (although that single submitter may have tested a large number of samples). AlleleFrequencies: Some submissions to dbSNP include allele frequencies and the study's sample size (i.e., the number of distinct chromosomes, which is two times the number of individuals assayed, a.k.a. 2N). dbSNP combines all available frequencies and counts from submitted SNPs that are clustered together into a reference SNP. You can configure this track such that the details page displays the function and coding differences relative to particular gene sets. Choose the gene sets from the list on the SNP configuration page displayed beneath this heading: On details page, show function and coding differences relative to. When one or more gene tracks are selected, the SNP details page lists all genes that the SNP hits (or is close to), with the same keywords used in the function category. The function usually agrees with NCBI's function, except when NCBI's functional annotation is relative to an XM_* predicted RefSeq (not included in the UCSC Genome Browser's RefSeq Genes track) and/or UCSC's functional annotation is relative to a transcript that is not in RefSeq. Insertions/Deletions dbSNP uses a class called 'in-del'. We compare the length of the reference allele to the length(s) of observed alleles; if the reference allele is shorter than all other observed alleles, we change 'in-del' to 'insertion'. Likewise, if the reference allele is longer than all other observed alleles, we change 'in-del' to 'deletion'. UCSC Re-alignment of flanking sequences dbSNP determines the genomic locations of SNPs by aligning their flanking sequences to the genome. UCSC displays SNPs in the locations determined by dbSNP, but does not have access to the alignments on which dbSNP based its mappings. Instead, UCSC re-aligns the flanking sequences to the neighboring genomic sequence for display on SNP details pages. While the recomputed alignments may differ from dbSNP's alignments, they often are informative when UCSC has annotated an unusual condition. Non-repetitive genomic sequence is shown in upper case like the flanking sequence, and a "|" indicates each match between genomic and flanking bases. Repetitive genomic sequence (annotated by RepeatMasker and/or the Tandem Repeats Finder with period Data Sources and Methods The data that comprise this track were extracted from database dump files and headers of fasta files downloaded from NCBI. The database dump files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/database/organism_data/ for hg19 and from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/database/organism_data/ for hg38. The fasta files were downloaded from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/rs_fasta/ for hg19 and from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b142_GRCh38/rs_fasta/ for hg38. Coordinates, orientation, location type and dbSNP reference allele data were obtained from b142_SNPContigLoc_N.bcp.gz and b142_ContigInfo_N.bcp.gz. (N = 105 for hg19, 106 for hg38) b142_SNPMapInfo_N.bcp.gz provided the alignment weights. Functional classification was obtained from b142_SNPContigLocusId_N.bcp.gz. The internal database representation uses dbSNP's function terms, but for display in SNP details pages, these are translated into Sequence Ontology terms. Validation status and heterozygosity were obtained from SNP.bcp.gz. SNPAlleleFreq.bcp.gz and ../shared/Allele.bcp.gz provided allele frequencies. For the human assembly, allele frequencies were also taken from SNPAlleleFreq_TGP.bcp.gz . Submitter handles were extracted from Batch.bcp.gz, SubSNP.bcp.gz and SNPSubSNPLink.bcp.gz. SNP_bitfield.bcp.gz provided miscellaneous properties annotated by dbSNP, such as clinically-associated. See the document dbSNP_BitField_v5.pdf for details. The header lines in the rs_fasta files were used for molecule type, class and observed polymorphism. Data Access The raw data can be explored interactively with the Table Browser, Data Integrator, or Variant Annotation Integrator. For automated analysis, the genome annotation can be downloaded from the downloads server for hg38 and hg19 (snp142*.txt.gz) or the public MySQL server. Please refer to our mailing list archives for questions and example queries, or our Data Access FAQ for more information. Orthologous Alleles (human assemblies only) For the human assembly, we provide a related table that contains orthologous alleles in the chimpanzee, orangutan and rhesus macaque reference genome assemblies. We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are a filtered list that meet the criteria: class = 'single' mapped position in the human reference genome is one base long aligned to only one location in the human reference genome not aligned to a chrN_random chrom biallelic (not tri- or quad-allelic) In some cases the orthologous allele is unknown; these are set to 'N'. If a lift was not possible, we set the orthologous allele to '?' and the orthologous start and end position to 0 (zero). Masked FASTA Files (human assemblies only) FASTA files that have been modified to use IUPAC ambiguous nucleotide characters at each base covered by a single-base substitution are available for download: GRCh37/hg19, GRCh38/hg38. Note that only single-base substitutions (no insertions or deletions) were used to mask the sequence, and these were filtered to exclude problematic SNPs. References Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783 
snp142Flagged Flagged SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142) Flagged by dbSNP as Clinically Assoc Variation Description This track contains information about a subset of the single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 142, available from ftp.ncbi.nih.gov/snp. Only SNPs flagged as clinically associated by dbSNP, mapped to a single location in the reference genome assembly, and not known to have a minor allele frequency of at least 1%, are included in this subset. Frequency data are not available for all SNPs, so this subset probably includes some SNPs whose true minor allele frequency is 1% or greater. The significance of any particular variant in this track should be interpreted only by a trained medical geneticist using all available information. For example, some variants are included in this track because of their inclusion in a Locus-Specific Database (LSDB) or mention in OMIM, but are not thought to be disease-causing, so inclusion of a variant in this track is not necessarily an indicator of risk. Again, all available information must be carefully considered by a qualified professional. The remainder of this page is identical on the following tracks: Common SNPs(142) - SNPs with &gt;= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(142) - SNPs &lt; 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(142) - SNPs mapping in more than one place on reference assembly. All SNPs(142) - all SNPs from dbSNP mapping to reference assembly. Interpreting and Configuring the Graphical Display Variants are shown as single tick marks at most zoom levels. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. Insertions are indicated by a single tick mark displayed between two nucleotides, single nucleotide polymorphisms are displayed as the width of a single base, and multiple nucleotide variants are represented by a block that spans two or more bases. On the track controls page, SNPs can be colored and/or filtered from the display according to several attributes: Class: Describes the observed alleles Single - single nucleotide variation: all observed alleles are single nucleotides (can have 2, 3 or 4 alleles) In-del - insertion/deletion Heterozygous - heterozygous (undetermined) variation: allele contains string '(heterozygous)' Microsatellite - the observed allele from dbSNP is a variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name instead of raw sequence, e.g., (Alu)/- No Variation - the submission reports an invariant region in the surveyed sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism (MNP) - the alleles are all of the same length, and length &gt; 1 Insertion - the polymorphism is an insertion relative to the reference assembly Deletion - the polymorphism is a deletion relative to the reference assembly Unknown - no classification provided by data contributor Validation: Method used to validate the variant (each variant may be validated by more than one method) By Frequency - at least one submitted SNP in cluster has frequency data submitted By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method By Submitter - at least one submitter SNP in cluster was validated by independent assay By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes By HapMap (human only) - submitted by HapMap project By 1000Genomes (human only) - submitted by 1000Genomes project Unknown - no validation has been reported for this variant Function: dbSNP's predicted functional effect of variant on RefSeq transcripts, both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*), not shown in UCSC Genome Browser. A variant may have more than one functional role if it overlaps multiple transcripts. These terms and definitions are from the Sequence Ontology (SO); click on a term to view it in the MISO Sequence Ontology Browser. Unknown - no functional classification provided (possibly intergenic) synonymous_variant - A sequence variant where there is no resulting change to the encoded amino acid (dbSNP term: coding-synon) intron_variant - A transcript variant occurring within an intron (dbSNP term: intron) downstream_gene_variant - A sequence variant located 3' of a gene (dbSNP term: near-gene-3) upstream_gene_variant - A sequence variant located 5' of a gene (dbSNP term: near-gene-5) nc_transcript_variant - A transcript variant of a non coding RNA gene (dbSNP term: ncRNA) stop_gained - A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript (dbSNP term: nonsense) missense_variant - A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid (dbSNP term: missense) stop_lost - A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript (dbSNP term: stop-loss) frameshift_variant - A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three (dbSNP term: frameshift) inframe_indel - A coding sequence variant where the change does not alter the frame of the transcript (dbSNP term: cds-indel) 3_prime_UTR_variant - A UTR variant of the 3' UTR (dbSNP term: untranslated-3) 5_prime_UTR_variant - A UTR variant of the 5' UTR (dbSNP term: untranslated-5) splice_acceptor_variant - A splice variant that changes the 2 base region at the 3' end of an intron (dbSNP term: splice-3) splice_donor_variant - A splice variant that changes the 2 base region at the 5' end of an intron (dbSNP term: splice-5) In the Coloring Options section of the track controls page, function terms are grouped into several categories, shown here with default colors: Locus: downstream_gene_variant, upstream_gene_variant Coding - Synonymous: synonymous_variant Coding - Non-Synonymous: stop_gained, missense_variant, stop_lost, frameshift_variant, inframe_indel Untranslated: 5_prime_UTR_variant, 3_prime_UTR_variant Intron: intron_variant Splice Site: splice_acceptor_variant, splice_donor_variant Molecule Type: Sample used to find this variant Genomic - variant discovered using a genomic template cDNA - variant discovered using a cDNA template Unknown - sample type not known Unusual Conditions (UCSC): UCSC checks for several anomalies that may indicate a problem with the mapping, and reports them in the Annotations section of the SNP details page if found: AlleleFreqSumNot1 - Allele frequencies do not sum to 1.0 (+-0.01). This SNP's allele frequency data are probably incomplete. DuplicateObserved, MixedObserved - Multiple distinct insertion SNPs have been mapped to this location, with either the same inserted sequence (Duplicate) or different inserted sequence (Mixed). FlankMismatchGenomeEqual, FlankMismatchGenomeLonger, FlankMismatchGenomeShorter - NCBI's alignment of the flanking sequences had at least one mismatch or gap near the mapped SNP position. (UCSC's re-alignment of flanking sequences to the genome may be informative.) MultipleAlignments - This SNP's flanking sequences align to more than one location in the reference assembly. NamedDeletionZeroSpan - A deletion (from the genome) was observed but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NamedInsertionNonzeroSpan - An insertion (into the genome) was observed but the annotation spans more than 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) NonIntegerChromCount - At least one allele frequency corresponds to a non-integer (+-0.010000) count of chromosomes on which the allele was observed. The reported total sample count for this SNP is probably incorrect. ObservedContainsIupac - At least one observed allele from dbSNP contains an IUPAC ambiguous base (e.g., R, Y, N). ObservedMismatch - UCSC reference allele does not match any observed allele from dbSNP. This is tested only for SNPs whose class is single, in-del, insertion, deletion, mnp or mixed. ObservedTooLong - Observed allele not given (length too long). ObservedWrongFormat - Observed allele(s) from dbSNP have unexpected format for the given class. RefAlleleMismatch - The reference allele from dbSNP does not match the UCSC reference allele, i.e., the bases in the mapped position range. RefAlleleRevComp - The reference allele from dbSNP matches the reverse complement of the UCSC reference allele. SingleClassLongerSpan - All observed alleles are single-base, but the annotation spans more than 1 base. (UCSC's re-alignment of flanking sequences to the genome may be informative.) SingleClassZeroSpan - All observed alleles are single-base, but the annotation spans 0 bases. (UCSC's re-alignment of flanking sequences to the genome may be informative.) Another condition, which does not necessarily imply any problem, is noted: SingleClassTriAllelic, SingleClassQuadAllelic - Class is single and three or four different bases have been observed (usually there are only two). Miscellaneous Attributes (dbSNP): several properties extracted from dbSNP's SNP_bitfield table (see dbSNP_BitField_v5.pdf for details) Clinically Associated (human only) - SNP is in OMIM and/or at least one submitter is a Locus-Specific Database. This does not necessarily imply that the variant causes any disease, only that it has been observed in clinical studies. Appears in OMIM/OMIA - SNP is mentioned in Online Mendelian Inheritance in Man for human SNPs, or Online Mendelian Inheritance in Animals for non-human animal SNPs. Some of these SNPs are quite common, others are known to cause disease; see OMIM/OMIA for more information. Has Microattribution/Third-Party Annotation - At least one of the SNP's