intronEst Spliced ESTs Mouse ESTs That Have Been Spliced mRNA and EST Description This track shows alignments between mouse expressed sequence tags (ESTs) in GenBank and the genome that show signs of splicing when aligned against the genome. ESTs are single-read sequences, typically about 500 bases in length, that usually represent fragments of transcribed genes. To be considered spliced, an EST must show evidence of at least one canonical intron (i.e., the genomic sequence between EST alignment blocks must be at least 32 bases in length and have GT/AG ends). By requiring splicing, the level of contamination in the EST databases is drastically reduced at the expense of eliminating many genuine 3' ESTs. For a display of all ESTs (including unspliced), see the mouse EST track. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, darker shading indicates a larger number of aligned ESTs. The strand information (+/-) indicates the direction of the match between the EST and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the EST display. For example, to apply the filter to all ESTs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only ESTs that match all filter criteria will be highlighted. If "or" is selected, ESTs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display ESTs that match the filter criteria. If "include" is selected, the browser will display only those ESTs that match the filter criteria. This track may also be configured to display base labeling, a feature that allows the user to display all bases in the aligning sequence or only those that differ from the genomic sequence. For more information about this option, go to the Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods To make an EST, RNA is isolated from cells and reverse transcribed into cDNA. Typically, the cDNA is cloned into a plasmid vector and a read is taken from the 5' and/or 3' primer. For most — but not all — ESTs, the reverse transcription is primed by an oligo-dT, which hybridizes with the poly-A tail of mature mRNA. The reverse transcriptase may or may not make it to the 5' end of the mRNA, which may or may not be degraded. In general, the 3' ESTs mark the end of transcription reasonably well, but the 5' ESTs may end at any point within the transcript. Some of the newer cap-selected libraries cover transcription start reasonably well. Before the cap-selection techniques emerged, some projects used random rather than poly-A priming in an attempt to retrieve sequence distant from the 3' end. These projects were successful at this, but as a side effect also deposited sequences from unprocessed mRNA and perhaps even genomic sequences into the EST databases. Even outside of the random-primed projects, there is a degree of non-mRNA contamination. Because of this, a single unspliced EST should be viewed with considerable skepticism. To generate this track, mouse ESTs from GenBank were aligned against the genome using blat. Note that the maximum intron length allowed by blat is 750,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. When a single EST aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence are displayed in this track. Credits This track was produced at UCSC from EST sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
cons30way Conservation 30-Way Multiz Alignment & Conservation Comparative Genomics Description This track shows multiple alignments of 30 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all species (vertebrate) and two subsets (Euarchontoglires and placental mammal). The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track. The species are divided into three different groups. The Euarchontoglires subset (10 species plus mouse), the placental mammal subset (19 species plus mouse), and all 30 vertebrate species together. These three measurements produce the same results in regions where only Euarchontoglires appear in the alignment. For other regions, the non-Euarchontoglires species can either boost the scores (if conserved) or decrease them (if non-conserved). The placental mammal conservation helps to identify sequences that are under different evolutionary pressures in mammals and non-mammal vertebrates. Euarchontoglires subset: mouse(mm9), rat(rn4), Guinea Pig(cavPor2), Rabbit(oryCun1), Human(hg18), Chimp(panTro2), Orangutan(ponAbe2), Rhesus(rheMac2), Marmoset(calJac1), Bushbaby(otoGar1), Tree Shrew(tupBel1) Placental mammal subset: the Euarchontoglires above plus: Shrew(sorAra1), Hedgehog(eriEur1), Dog(canFam2), Cat(felCat3), Horse(equCab1), Cow(bosTau3), Armadillo(dasNov1), Elephant(loxAfr1), Tenrec(echTel1) Vertebrates: the placentals and Euarchontoglires above plus: Opossum(monDom4), Platypus(ornAna1), Chicken(galGal3), Lizard(anoCar1), Frog(xenTro2), Tetraodon(tetNig1), Fugu(fr2), Stickleback(gasAcu1), Medaka(oryLat1), Zebrafish(danRer5) PhastCons (which has been used in previous Conservation tracks) is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites). Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1. Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data, and both were run with the same parameters for each species set (vertebrates, placental mammals, and Euarchontoglires). Thus, in regions in which only Euarchontoglires appear in the alignment, all three sets of scores will be the same, but in regions in which additional species are available, the mammalian and/or vertebrate scores may differ from the Euarchontoglires scores. The alternative plots help to identify sequences that are under different evolutionary pressures in, say, Euarchontoglires and non-Euarchontoglires, or mammals and non-mammals. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. The conservation measurements were created using the phastCons package from Adam Siepel at Cold Spring Harbor Laboratory. Details of the alignment parameters are noted in the genomewiki Mm9 multiple alignment page. The species aligned for this track include the reptile, amphibian, bird, and fish clades, as well as marsupial, monotreme (platypus), and placental mammals. Compared to the previous 17-vertebrate alignment, this track includes 13 new species and 4 species with updated sequence assemblies (Table 1). The new species consist of seven high-coverage (5-8.5X) assemblies (orangutan, marmoset, horse, platypus, lizard, and two teleost fish: stickleback and medaka) and six low-coverage (2X) genome assemblies from mammalian species selected for sampling by NHGRI (bushbaby, tree shrew, guinea pig, hedgehog, common shrew, and cat). The cow, chicken, fugu, and zebrafish assemblies in this track have been updated from those used in the previous 17-species alignment. UCSC has repeatmasked and aligned the low-coverage genome assemblies, and provides the sequence for download; however, we do not construct genome browsers for them. Missing sequence in the low-coverage assemblies is highlighted in the track display by regions of yellow when zoomed out and Ns displayed at base level (see Gap Annotation, below). OrganismSpeciesRelease dateUCSC version MouseMus musculus Jul 2007 mm9 ArmadilloDasypus novemcinctusMay 2005 dasNov1* BushbabyOtolemur garnettiDec 2006 otoGar1* CatFelis catus Mar 2006 felCat3 ChickenGallus gallus May 2006 galGal3 ChimpanzeePan troglodytes Mar 2006 panTro2 CowBos taurus Aug 2006 bosTau3 DogCanis familiaris May 2005 canFam2 ElephantLoxodonta africanaMay 2005 loxAfr1* FrogXenopus tropicalis Aug 2005 xenTro2 FuguTakifugu rubripes Oct 2004 fr2 Guinea pigCavia porcellusOct 2005 cavPor2* HedgehogErinaceus europaeusJune 2006 eriEur1* HorseEquus caballus Jan 2007 equCab1 HumanHomo sapiens Mar 2006 hg18 LizardAnolis carolinensis Feb 2007 anoCar1 MarmosetCallithrix jacchusJune 2007 calJac1 MedakaOryzias latipes Apr 2006oryLat1* OpossumMonodelphis domestica Jan 2006 monDom4 OrangutanPongo pygmaeus abelii July 2007ponAbe2 PlatypusOrnithorhychus anatinus Mar 2007 ornAna1 RabbitOryctolagus cuniculusMay 2005 oryCun1* RatRattus norvegicus Nov 2004 rn4 RhesusMacaca mulatta Jan 2006 rheMac2 ShrewSorex araneusJune 2006 sorAra1* SticklebackGasterosteus aculeatus Feb 2006 gasAcu1 TenrecEchinops telfairiJuly 2005 echTel1* TetraodonTetraodon nigroviridis Feb 2004 tetNig1 Tree shrewTupaia belangeriDec 2006 tupBel1* ZebrafishDanio rerio July 2007 danRer5 Table 1. Genome assemblies included in the 30-way Conservation track. * Data download only, browser not available. Downloads for data in this track are available: Multiz alignments (MAF format), and phylogenetic trees PhyloP conservation (WIG format) PhastCons conservation (WIG format) Display Conventions and Configuration In full and pack display modes, conservation scores are displayed as wiggle tracks (histograms) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options. Pairwise alignments of each species to the mouse genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons. Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults). By default, the following 8 species are included in the pairwise display: rat, human, orangutan, dog, horse, opossum, chicken, and stickleback. Note that excluding species from the pairwise display does not alter the the conservation score display. To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment. Gap Annotation The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used: Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the mouse genome or a lineage-specific deletion between the aligned blocks in the aligning species. Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species. Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species. Genomic Breaks Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows: Vertical blue bar: Represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement. Green square brackets: Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the mouse genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence. Base Level When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the mouse sequence at those alignment positions relative to the longest non-mouse sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+". Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes: No codon translation: The gene annotation is not used; the bases are displayed without translation. Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment. Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding. Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation. Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation. Gene TrackSpecies Known Geneshuman, mouse Ensembl Genesrat, rhesus, chimp, dog, opossum, platypus, zebrafish, fugu, stickleback, medaka RefSeq Genescow, frog mRNAsorangutan, elephant, rabbit, cat, horse, chicken, lizard, armadillo, tetraodon Nonemarmoset, bushbaby, tree shrew, guinea pig, shrew, hedgehog, tenrec Table 2. Gene tracks used for codon translation. Methods Pairwise alignments with the mouse genome were generated for each species using lastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. The scoring matrix and parameters for pairwise alignment and chaining were tuned for each species based on phylogenetic distance from the reference. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks. An additional filtering step was introduced in the generation of the 30-way conservation track to reduce the number of paralogs and pseudogenes from the high-quality assemblies and the suspect alignments from the low-quality assemblies: the pairwise alignments of high-quality mammalian sequences (placental and marsupial) were filtered based on synteny; those for 2X mammalian genomes were filtered to retain only alignments of best quality in both the target and query ("reciprocal best"). The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display. Phylogenetic Tree Model Both phastCons and phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The vertebrate tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 30-way alignment (msa_view). The 4d sites were derived from the Oct 2005 Gencode Reference Gene set, which was filtered to select single-coverage long transcripts. The placental mammal tree model and the Euarchontoglires tree model were extracted from the vertebrate model. The phastCons parameters were tuned to produce 5% conserved elements in the genome for the vertebrate conservation measurement. This parameter set (expected-length=45, target-coverage=.3, rho=.31) was then used to generate the placental mammal and Euarchontoglires conservation scoring. The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, note that phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005. PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps. PhyloP Conservation The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements ( http://compgen.cshl.edu/phast/). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC). Conserved Elements The conserved elements were predicted by running phastCons with the --viterbi option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full". Credits This track was created using the following programs: Alignment tools: lastz (formerly blastz) and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC). MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC Tree image generator: phyloPng by Galt Barber, UCSC Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community as of March 2007. References Phylo-HMMs, phastCons, and phyloP: Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911 Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216 Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396 Chain/Net: Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Multiz: Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317 Lastz (formerly Blastz): Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 Phylogenetic Tree: Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51. PMID: 11743200 
cons30wayViewalign Multiz Alignments 30-Way Multiz Alignment & Conservation Comparative Genomics 
multiz30way Multiz Align Multiz Alignments of 30 Vertebrates Comparative Genomics Description This track shows multiple alignments of 30 vertebrate species and three measures of evolutionary conservation -- conservation across all 30 species, an alternative measurement restricted to the euarchontoglires subset (10 species plus mouse) of the alignment, and a measurement restricted to the placental mammal subset (19 species plus mouse) of the alignment. These three measurements produce the same results in regions where only euarchontoglires appear in the alignment. For other regions, the non-euarchontoglires species can either boost the scores (if conserved) or decrease them (if non-conserved). The placental mammal conservation helps to identify sequences that are under different evolutionary pressures in mammals and non-mammal vertebrates. Euarchontoglire subset: mouse(mm9), rat(rn4), Guinea Pig(cavPor2), Rabbit(oryCun1), Human(hg18), Chimp(panTro2), Orangutan(ponAbe2), Rhesus(rheMac2), Marmoset(calJac1), Bushbaby(otoGar1), Tree Shrew(tupBel1) Placental mammal subset: the euarchontoglires above plus: Shrew(sorAra1), Hedgehog(eriEur1), Dog(canFam2), Cat(felCat3), Horse(equCab1), Cow(bosTau3), Armadillo(dasNov1), Elephant(loxAfr1), Tenrec(echTel1) Vertebrates: the placentals and euarchontoglires above plus: Opossum(monDom4), Platypus(ornAna1), Chicken(galGal3), Lizard(anoCar1), Frog(xenTro2), Tetraodon(tetNig1), Fugu(fr2), Stickleback(gasAcu1), Medaka(oryLat1), Zebrafish(danRer5) The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. The conservation measurements were created using the phastCons package from Adam Siepel at Cold Spring Harbor Laboratory. Details of the alignment parameters are noted in the genomewiki Mm9 multiple alignment page. The species aligned for this track include the reptile, amphibian, bird, and fish clades, as well as marsupial, monotreme (platypus), and placental mammals. Compared to the previous 17-vertebrate alignment, this track includes 13 new species and 4 species with updated sequence assemblies (Table 1). The new species consist of seven high-coverage (5-8.5X) assemblies (orangutan, marmoset, horse, platypus, lizard, and two teleost fish: stickleback and medaka) and six low-coverage (2X) genome assemblies from mammalian species selected for sampling by NHGRI (bushbaby, tree shrew, guinea pig, hedgehog, common shrew, and cat). The cow, chicken, fugu, and zebrafish assemblies in this track have been updated from those used in the previous 17-species alignment. UCSC has repeatmasked and aligned the low-coverage genome assemblies, and provides the sequence for download; however, we do not construct genome browsers for them. Missing sequence in the low-coverage assemblies is highlighted in the track display by regions of yellow when zoomed out and Ns displayed at base level (see Gap Annotation, below). OrganismSpeciesRelease dateUCSC version MouseMus musculus Jul 2007 mm9 ArmadilloDasypus novemcinctusMay 2005 dasNov1 BushbabyOtolemur garnettiDec 2006 otoGar1 CatFelis catus Mar 2006 felCat3 ChickenGallus gallus May 2006 galGal3 ChimpanzeePan troglodytes Mar 2006 panTro2 CowBos taurus Aug 2006 bosTau3 DogCanis familiaris May 2005 canFam2 ElephantLoxodonta africanaMay 2005 loxAfr1 FrogXenopus tropicalis Aug 2005 xenTro2 FuguTakifugu rubripes Oct 2004 fr2 Guinea pigCavia porcellusOct 2005 cavPor2 HedgehogErinaceus europaeusJune 2006 eriEur1 HorseEquus caballus Jan 2007 equCab1 HumanHomo sapiens Mar 2006 hg18 LizardAnolis carolinensis Feb 2007 anoCar1 MarmosetCallithrix jacchusJune 2007 calJac1 MedakaOryzias latipes Apr 2006oryLat1 OpossumMonodelphis domestica Jan 2006 monDom4 OrangutanPongo pygmaeus abelii July 2007ponAbe2 PlatypusOrnithorhychus anatinus Mar 2007 ornAna1 RabbitOryctolagus cuniculusMay 2005 oryCun1 RatRattus norvegicus Nov 2004 rn4 RhesusMacaca mulatta Jan 2006 rheMac2 ShrewSorex araneusJune 2006 sorAra1 SticklebackGasterosteus aculeatus Feb 2006 gasAcu1 TenrecEchinops telfairiJuly 2005 echTel1 TetraodonTetraodon nigroviridis Feb 2004 tetNig1 Tree shrewTupaia belangeriDec 2006 tupBel1 ZebrafishDanio rerio July 2007 danRer5 Table 1. Genome assemblies included in the 30-way Conservation track. Display Conventions and Configuration The track configuration options allow the user to display either the vertebrate or placental mammal conservation scores, or both simultaneously. In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options. Pairwise alignments of each species to the mouse genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons. Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults). By default, the following 8 species are included in the pairwise display: rat, human, orangutan, dog, horse, opossum, chicken, and stickleback. Note that excluding species from the pairwise display does not alter the the conservation score display. To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment. Gap Annotation The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used: Single line: no bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the mouse genome or a lineage-specific deletion between the aligned blocks in the aligning species. Double line: aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species. Pale yellow coloring: aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species. Genomic Breaks Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows: Vertical blue bar: represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement. Green square brackets: enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the mouse genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence. Base Level When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the mouse sequence at those alignment positions relative to the longest non-mouse sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+". Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes: No codon translation: the gene annotation is not used; the bases are displayed without translation. Use default species reading frames for translation: the annotations from the genome displayed in the Default species for translation; pull-down menu are used to translate all the aligned species present in the alignment. Use reading frames for species if available, otherwise no translation: codon translation is performed only for those species where the region is annotated as protein coding. Use reading frames for species if available, otherwise use default species: codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation. Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation. Gene TrackSpecies Known Geneshuman, mouse Ensembl Genesrat, rhesus, chimp, dog, opossum, platypus, zebrafish, fugu, stickleback, medaka RefSeq Genescow, frog mRNAsorangutan, elephant, rabbit, cat, horse, chicken, lizard, armadillo, tetraodon Nonemarmoset, bushbaby, tree shrew, guinea pig, shrew, hedgehog, tenrec Table 2. Gene tracks used for codon translation. Methods Pairwise alignments with the mouse genome were generated for each species using blastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. The scoring matrix and parameters for pairwise alignment and chaining were tuned for each species based on phylogenetic distance from the reference. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks. An additional filtering step was introduced in the generation of the 30-way conservation track to reduce the number of paralogs and pseudogenes from the high-quality assemblies and the suspect alignments from the low-quality assemblies: the pairwise alignments of high-quality mammalian sequences (placental and marsupial) were filtered based on synteny; those for 2X mammalian genomes were filtered to retain only alignments of best quality in both the target and query ("reciprocal best"). The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display. Conservation scoring was performed using the PhastCons package (A. Siepel), which computes conservation based on a two-state phylogenetic hidden Markov model (HMM). PhastCons measurements rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The vertebrate tree model for this track was generated using the phyloFit program from the phastCons package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 30way alignment (msa_view). The 4d sites were derived from the Oct 2005 Gencode Reference Gene set, which was filtered to select single-coverage long transcripts. A second, mammalian tree model including only placental mammals was used to generate the placental mammal conservation scoring. The phastCons parameters were tuned to produce 5% conserved elements in the genome for the vertebrate conservation measurement. This parameter set (expected-length=45, target-coverage=.3, rho=.31) was then used to generate the placental mammal conservation scoring. The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, note that phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005. PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps. Credits This track was created using the following programs: Alignment tools: blastz and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC Conservation scoring: PhastCons, phyloFit, tree_doctor, msa_view by Adam Siepel while at UCSC, now at Cold Spring Harbor Laboratory MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC Tree image generator: phyloPng by Galt Barber, UCSC Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community as of March 2007. References Phylo-HMMs and phastCons: Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911 Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216 Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396 Chain/Net: Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Multiz: Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317 Blastz: Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 Phylogenetic Tree: Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51. PMID: 11743200 
cons30wayViewphastcons Element Conservation (phastCons) 30-Way Multiz Alignment & Conservation Comparative Genomics 
phastCons30way Vertebrate Cons Vertebrate Conservation by PhastCons Comparative Genomics 
phastCons30wayPlacental Mammal Cons Placental Mammal Conservation by PhastCons Comparative Genomics 
phastCons30wayEuarch Euarch Cons Euarchontoglires Conservation by PhastCons Comparative Genomics 
cons30wayViewelements Conserved Elements 30-Way Multiz Alignment & Conservation Comparative Genomics 
phastConsElements30way Vertebrate El PhastCons Vertebrate Conserved Elements, 30-way Multiz Alignment Comparative Genomics 
phastConsElements30wayPlacental Mammal El PhastCons Placental Mammal Conserved Elements, 30-way Multiz Alignment Comparative Genomics 
phastConsElements30wayEuarch Euarch El PhastCons Euarchontoglires Conserved Elements, 30-way Multiz Alignment Comparative Genomics 
cons30wayViewphyloP Basewise Conservation (phyloP) 30-Way Multiz Alignment & Conservation Comparative Genomics 
phyloP30wayAll Vertebrate Cons Vertebrate Basewise Conservation by PhyloP Comparative Genomics 
phyloP30wayPlacental Mammal Cons Placental Mammal Basewise Conservation by PhyloP Comparative Genomics 
phyloP30wayEuarch Euarch Cons Euarchontoglires Basewise Conservation by PhyloP Comparative Genomics 
cpgIslandExt CpG Islands CpG Islands (Islands < 300 Bases are Light Green) Expression and Regulation Description CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole. The unmasked version of the track displays potential CpG islands that exist in repeat regions and would otherwise not be visible in the repeat masked version. By default, only the masked version of the track is displayed. To view the unmasked version, change the visibility settings in the track controls at the top of this page. Methods CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. Each segment was then evaluated for the following criteria: GC content of 50% or greater length greater than 200 bp ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the number of Gs and Cs in the segment The entire genome sequence, masking areas included, was used for the construction of the track Unmasked CpG. The track CpG Islands is constructed on the sequence after all masked sequence is removed. The CpG count is the number of CG dinucleotides in the island. The Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length. The ratio of observed to expected CpG is calculated according to the formula (cited in Gardiner-Garden et al. (1987)): Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence. The calculation of the track data is performed by the following command sequence: twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \ | cpg_lh /dev/stdin 2&gt; cpg_lh.err \ | awk '{&dollar;2 = &dollar;2 - 1; width = &dollar;3 - &dollar;2; printf("%s\t%d\t%s\t%s %s\t%s\t%s\t%0.0f\t%0.1f\t%s\t%s\n", &dollar;1, &dollar;2, &dollar;3, &dollar;5, &dollar;6, width, &dollar;6, width*&dollar;7*0.01, 100.0*2*&dollar;6/width, &dollar;7, &dollar;9);}' \ | sort -k1,1 -k2,2n &gt; cpgIsland.bed The unmasked track data is constructed from twoBitToFa -noMask output for the twoBitToFa command. Data access CpG islands and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. All the tables can also be queried directly from our public MySQL servers, with more information available on our help page as well as on our blog. The source for the cpg_lh program can be obtained from src/utils/cpgIslandExt/. The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file") Credits This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished). References Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447 
cpgIslandSuper CpG Islands CpG Islands (Islands < 300 Bases are Light Green) Expression and Regulation Description CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole. The unmasked version of the track displays potential CpG islands that exist in repeat regions and would otherwise not be visible in the repeat masked version. By default, only the masked version of the track is displayed. To view the unmasked version, change the visibility settings in the track controls at the top of this page. Methods CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. Each segment was then evaluated for the following criteria: GC content of 50% or greater length greater than 200 bp ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the number of Gs and Cs in the segment The entire genome sequence, masking areas included, was used for the construction of the track Unmasked CpG. The track CpG Islands is constructed on the sequence after all masked sequence is removed. The CpG count is the number of CG dinucleotides in the island. The Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length. The ratio of observed to expected CpG is calculated according to the formula (cited in Gardiner-Garden et al. (1987)): Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence. The calculation of the track data is performed by the following command sequence: twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \ | cpg_lh /dev/stdin 2&gt; cpg_lh.err \ | awk '{&dollar;2 = &dollar;2 - 1; width = &dollar;3 - &dollar;2; printf("%s\t%d\t%s\t%s %s\t%s\t%s\t%0.0f\t%0.1f\t%s\t%s\n", &dollar;1, &dollar;2, &dollar;3, &dollar;5, &dollar;6, width, &dollar;6, width*&dollar;7*0.01, 100.0*2*&dollar;6/width, &dollar;7, &dollar;9);}' \ | sort -k1,1 -k2,2n &gt; cpgIsland.bed The unmasked track data is constructed from twoBitToFa -noMask output for the twoBitToFa command. Data access CpG islands and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. All the tables can also be queried directly from our public MySQL servers, with more information available on our help page as well as on our blog. The source for the cpg_lh program can be obtained from src/utils/cpgIslandExt/. The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file") Credits This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished). References Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447 
pubs Publications Publications: Sequences in Scientific Articles Literature Description This track is based on text-mining of full-text biomedical articles and includes two types of subtracks: Sequences found in publications, grouped by article and searched in genomes with BLAT Identifiers in publications that directly relate to chromosome locations (e.g., gene symbols, SNP identifiers, etc) Both sources of information are linked to the respective articles. Background information on how permission to full-text data was obtained can be found on the project website. Display Convention and Configuration The sequence subtrack indicates the location of sequences in publications mapped back to the genome, annotated with the first author and the year of the publication. All matches of one article are grouped ("chained") together. Article titles are shown when you move the mouse cursor over the features. Thicker parts of the features (exons) represent matching sequences, connected by thin lines to matches from the same article within 30 kbp. The subtrack "individual sequence matches" activates automatically when the user clicks a sequence match and follows the link "Show sequence matches individually" from the details page. Mouse-overs show flanking text around the sequence, and clicking features links to BLAT alignments. All other subtracks (i.e. bands, genes, SNPs) show the number of matching articles as the feature description. Clicking on them shows the sentences and sections in articles where the identifiers were found. The track configuration includes a keyword and year filter. Keywords are space-separated and are searched in the article's title, author list, and abstract. Data The track is based on text from biomedical research articles, obtained as part of the UCSC Genocoding Project. The current dataset consists of about 600,000 files (main text and supplementary files) from PubMed Central (Open-Access set) and around 6 million text files (main text) from Elsevier (as part of the Sciverse Apps program). Methods All file types (including XML, raw ASCII, PDFs and various Microsoft Office formats (Excel, Word, PowerPoint)) were converted to text. The results were processed to find groups of words that look like DNA/RNA sequences or words that look like protein sequences. These were then mapped with BLAT to the human genome and these model organisms: mouse (mm9), rat (rn4), zebrafish (danRer6), Drosophila melanogaster (dm3), X. tropicalis (xenTro2), Medaka (oryLat2), C. intestinalis (ci2), C. elegans (ce6) and yeast (sacCer2). The pipeline roughly proceeds through these steps: For sequences, the best match across all genomes is used, if it is longer than 17 bp and matches at 90% identity. Two sets of BLAT parameters are tried, the default ones for sequences longer than 25 bp, very sensitive ones (stepSize=5) for shorter sequences. Sequences are mapped to genomic DNA. Those that do not match are mapped to RefSeq cDNAs. Hits from the same article that are closer than 30 kbp are joined into one feature (shown as exon-blocks on the browser). All parts of a joined feature have to match at least 25 bp. Non-unique hits are kept in the joined feature with the most members. Joined features with identical members in two different genomes are kept in both genomes. Note that due to the 90% identity filter, some sequences do not match anywhere in the genome. Examples include primers with added restriction sites, mutation primers, or any other sequence that joins or mixes two pieces of genomic DNA not part of RefSeq. Also note that some gene symbols correspond to English words which can sometimes lead to many false positives. Credits Software and processing by Maximilian Haeussler. UCSC Track visualisation by Larry Meyer and Hiram Clawson. Elsevier support by Max Berenstein, Raphael Sidi, Judd Dunham, Scott Robbins and colleagues. Original version written at the Bergman Lab, University of Manchester, UK. Testing by Mary Mangan, OpenHelix Inc, and Greg Roe, UCSC. Feedback Please send ideas, comments or feedback on this track to &#109;a&#120;&#64;&#115;&#111;&#101;.uc&#115;&#99;.e&#100;&#117;. We are very interested in getting access to more articles from publishers for this dataset; see the project website. References Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM, Open Regulatory Annotation Consortium. Text-mining assisted regulatory annotation. Genome Biol. 2008;9(2):R31. PMID: 18271954; PMC: PMC2374703 Haeussler M, Gerner M, Bergman CM. Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics. 2011 Apr 1;27(7):980-6. PMID: 21325301; PMC: PMC3065681 Van Noorden R. Trouble at the text mine. Nature. 2012 Mar 7;483(7388):134-5. 
pubsBlat Sequences Sequences in Articles: PubmedCentral and Elsevier Literature 
pubsBlatPsl Indiv. Seq. Matches Individual Sequence Matches of One Selected Article from Sequences Track Literature 
snp128 SNPs (128) Simple Nucleotide Polymorphisms (dbSNP build 128) Variation and Repeats Description This track contains information about single nucleotide polymorphisms and small insertions and deletions (indels) &mdash; collectively Simple Nucleotide Polymorphisms &mdash; from dbSNP build 128, available from ftp.ncbi.nih.gov/snp. 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. The configuration categories reflect the following definitions (not all categories apply to this assembly): 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 variation in counts of short tandem repeats Named - the observed allele from dbSNP is given as a text name No Variation - no variation asserted for sequence Mixed - the cluster contains submissions from multiple classes Multiple Nucleotide Polymorphism - alleles of the same length, length > 1, and from set of {A,T,C,G} 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 - validated by HapMap 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. As of dbSNP build 128, several functional terms have been replaced by more detailed functional terms; for filtering and coloring, the new function terms are grouped into more general categories: Locus Region - variation is 3' to and within 500 bases of a transcript, or is 5' to and within 2000 bases of a transcript (dbSNP terms: near-gene-3 and near-gene-5 replace older term locus; Sequence Ontology terms: downstream_gene_variant, upstream_gene_variant) Coding - Synonymous - no change in peptide for allele with respect to reference assembly (dbSNP term: coding-synon; Sequence Ontology term: synonymous_variant) Coding - Non-Synonymous - change in peptide for allele with respect to reference assembly (dbSNP terms: nonsense, missense, frameshift replace older term coding-nonsynon; Sequence Ontology terms: stop_gained, missense_variant, frameshift_variant) Untranslated - variation in transcript, but not in coding region interval (dbSNP terms: untranslated-3, untranslated-5 replace older term untranslated; Sequence Ontology terms: 3_prime_UTR_variant, 5_prime_UTR_variant) Intron - variation in intron, but not in first two or last two bases of intron (dbSNP term: intron; Sequence Ontology term: intron_variant) Splice Site - variation in first two or last two bases of intron (dbSNP terms: splice-3, splice-5 replace older term splice-site; Sequence Ontology terms: splice_acceptor_variant, splice_donor_variant) Reference (coding) - one of the observed alleles of a SNP in a coding region matches the reference assembly (dbSNP term: cds-reference; Sequence Ontology term: coding_sequence_variant) Unknown - no known functional classification 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 Average heterozygosity: Calculated by dbSNP as described here 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 3. 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, but can sometimes give a bit more detail (e.g. more detail about how close a near-gene SNP is to a nearby gene). 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 Annotations UCSC checks for several unusual conditions that may indicate a problem with the mapping, and reports them in the Annotations section if found: The dbSNP reference allele is not the same as the UCSC reference allele, i.e. the bases in the mapped position range. Class is single, in-del, mnp or mixed and the UCSC reference allele does not match any observed allele. In NCBI's alignment of flanking sequences to the genome, part of the flanking sequence around the SNP does not align to the genome. Class is single, but the size of the mapped SNP is not one base. Class is named and indicates an insertion or deletion, but the size of the mapped SNP implies otherwise. Class is single and the format of observed alleles is unexpected. The length of the observed allele(s) is not available because it is too long. Multiple distinct insertion SNPs have been mapped to this location. At least one observed allele contains an ambiguous IUPAC base (e.g. R, Y, N). Another condition, which does not necessarily imply any problem, is noted: Class is single and SNP is tri-allelic or quad-allelic. 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. Data Sources 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/ (e.g. for Human, organism_tax_id = human_9606). 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 b128_SNPContigLoc_36_2.bcp.gz and b128_SNPContigInfo_36_2.bcp.gz. b128_SNPMapInfo_36_2.bcp.gz provided the alignment weights. Functional classification was obtained from b128_SNPContigLocusId_36_2.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. 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 can be downloaded from the downloads server for mm9 and hg18 (snp128*.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 only) Beginning with the March 2006 human assembly, we provide a related table that contains orthologous alleles in the chimpanzee and rhesus macaque 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' chromEnd = chromStart + 1 align to just one location are not aligned to a chrN_random chrom are 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 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 here. 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. 
stsMapMouseNew STS Markers STS Markers on Genetic and Radiation Hybrid Maps Mapping and Sequencing Description This track shows locations of Sequence Tagged Sites (STS) along the mouse draft assembly. These markers have been mapped using either genetic mapping (WICGR Mouse Genetic Map, MGD Genetic Map) or radiation hybridization mapping (Whitehead/MRC RH Map) techniques. Additional data on the individual maps can be found at the following links: NCBI UniSTS Mouse Genome Informatics (MGI) By default all genetic map markers are shown as blue; only radiation hybrid markers and markers that are neither genetic nor radiation hybrid are shown as black; markers that map to more than one position are shown in lighter colors. Users can choose a color to highlight a subset of markers of interest from the Filter options in STS Markers Track Setting page. Methods Positions of STS markers are determined using both full sequences and primer information. Full sequences are aligned using blat, while ePCR is used to find locations using primer information. Using the Filter The track filter can be used to change the color or include/exclude a set of map data within the track. This is helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: In the pulldown menu, select the map whose data you would like to highlight or exclude in the display. By default, the &quot;All Genetic&quot; option is selected. Choose the color or display characteristic that will be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display data from the map selected in the pulldown list. If &quot;include&quot; is selected, the browser will display only data from the selected map. When you have finished configuring the filter, click the Submit button. Credits This track was designed and implemented by Terry Furey and Yontao Lu. Many thanks to Whitehead Institute (Broad Institute) and Jackson Lab for contributing the data. 
knownGene UCSC Genes UCSC Genes (RefSeq, GenBank, tRNAs & Comparative Genomics) Genes and Gene Predictions Description The UCSC Genes track shows gene predictions based on data from RefSeq, GenBank, and the tRNA Genes track. This is a moderately conservative set of predictions, requiring the support of one GenBank RNA sequence plus at least one additional line of evidence. The RefSeq RNAs are an exception to this, requiring no additional evidence. The track includes both protein-coding and putative non-coding transcripts. Some of these non-coding transcripts may actually code for protein, but the evidence for the associated protein is weak at best. Compared to RefSeq, this gene set has generally about 10% more protein-coding genes, approximately five times as many putative non-coding genes, and about twice as many splice variants. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track in general follows the display conventions for gene prediction tracks. The exons for putative noncoding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker. The following color key is used: Black -- feature has a corresponding entry in the Protein Databank (PDB) Dark blue -- transcript has been reviewed or validated by either the RefSeq or SwissProt staff Medium blue -- other RefSeq transcripts Light blue -- non-RefSeq transcripts This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. Click here for more information about this feature. Methods The UCSC Genes are built using a multi-step pipeline: RefSeq and GenBank RNAs are aligned to the genome with BLAT, keeping only the best alignments for each RNA and discarding alignments of less than 98% identity. Alignments are broken up at non-intronic gaps, with small isolated fragments thrown out. A splicing graph is created for each set of overlapping alignments. This graph has an edge for each exon or intron, and a vertex for each splice site, start, and end. Each RNA that contributes to an edge is kept as evidence for that edge. A similar splicing graph is created in the mouse, based on mouse RNA and ESTs. If the mouse graph has an edge that is orthologous to an edge in the human graph, that is added to the evidence for the human edge. If an edge in the splicing graph is supported by two or more human ESTs, it is added as evidence for the edge. If there is an Exoniphy prediction for an exon, that is added as evidence. The graph is traversed to generate all unique transcripts. The traversal is guided by the initial RNAs to avoid a combinatorical explosion in alternative splicing. All refSeq transcripts are output. For other multi-exon transcripts to be output, an edge supported by at least one additional line of evidence beyond the RNA is required. Single-exon genes require either two RNAs or two additional lines of evidence beyond the single RNA. Protein predictions are generated. For non-RefSeq transcripts we use the txCdsPredict program to determine if the transcript is protein-coding and if so, the locations of the start and stop codons. The program weighs as positive evidence the length of the protein, the presence of a Kozak consensus sequence at the start codon, and the length of the orthologous predicted protein in other species. As negative evidence it considers nonsense-mediated decay and start codons in any frame upstream of the predicted start codon. For RefSeq transcripts the RefSeq protein prediction is used. The corresponding UniProt protein is found, if any. The transcript is assigned a permanent "uc" accession. Credits The UCSC Genes track was produced at UCSC using a computational pipeline developed by Jim Kent, Chuck Sugnet and Mark Diekhans. It is based on data from NCBI RefSeq, UniProt (including TrEMBL and TrEMBL-NEW) and GenBank. Our thanks to the people running these databases and to the scientists worldwide who have made contributions to them. Data Use Restrictions The UniProt data have the following terms of use, UniProt copyright(c) 2002 - 2004 UniProt consortium: For non-commercial use, all databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy. For commercial use, all databases and documents in the UniProt FTP directory except the files ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.xml.gz may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy. More information for commercial users can be found here. From January 1, 2005, all databases and documents in the UniProt FTP directory may be copied and redistributed freely by all entities, without advance permission, provided that this copyright statement is reproduced with each copy. References Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC Known Genes. Bioinformatics. 2006 May 1;22(9):1036-46. PMID: 16500937 Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
ensGene Ensembl Genes Ensembl Genes Genes and Gene Predictions Description These gene predictions were generated by Ensembl. For more information on the different gene tracks, see our Genes FAQ. Methods For a description of the methods used in Ensembl gene predictions, please refer to Hubbard et al. (2002), also listed in the References section below. Data access Ensembl Gene data can be explored interactively using the Table Browser or the Data Integrator. For local downloads, the genePred format files for mm9 are available in our downloads directory as ensGene.txt.gz or in our genes download directory in GTF format. For programmatic access, the data can be queried from the REST API or directly from our public MySQL servers. Instructions on this method are available on our MySQL help page and on our blog. Previous versions of this track can be found on our archive download server. Credits We would like to thank Ensembl for providing these gene annotations. For more information, please see Ensembl&#39s genome annotation page. References Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41. PMID: 11752248; PMC: PMC99161 
refSeqComposite NCBI RefSeq RefSeq genes from NCBI Genes and Gene Predictions Description The NCBI RefSeq Genes composite track shows mouse protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). All subtracks use coordinates provided by RefSeq, except for the UCSC RefSeq track, which UCSC produces by realigning the RefSeq RNAs to the genome. This realignment may result in occasional differences between the annotation coordinates provided by UCSC and NCBI. For RNA-seq analysis, we advise using NCBI aligned tables like RefSeq All or RefSeq Curated. See the Methods section for more details about how the different tracks were created. Please visit NCBI's Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track is a composite track that contains differing data sets. To show only a selected set of subtracks, uncheck the boxes next to the tracks that you wish to hide. Note: Not all subtracts are available on all assemblies. The possible subtracks include: RefSeq aligned annotations and UCSC alignment of RefSeq annotations RefSeq All &ndash; all curated and predicted annotations provided by RefSeq. RefSeq Curated &ndash; subset of RefSeq All that includes only those annotations whose accessions begin with NM, NR, NP or YP. (NP and YP are used only for protein-coding genes on the mitochondrion; YP is used for human only.) They were manually curated, based on publications describing transcripts and manual reviews of evidence which includes EST and full-length cDNA alignments, protein sequences, splice sites and any other evidence available in databases or the scientific literature. The resulting sequences can differ from the genome, they exist independently from a particular human genome build, and so must be aligned to the genome to create a track. The "RefSeq Curated" track is NCBI's mapping of these transcripts to the genome. Another alignment track exists for these, the "UCSC RefSeq" track (see beloow). RefSeq Predicted &ndash; subset of RefSeq All that includes those annotations whose accessions begin with XM or XR. They were predicted based on protein, cDNA, EST and RNA-seq alignments to the genome assembly by the NCBI Gnomon prediction software. RefSeq Other &ndash; all other annotations produced by the RefSeq group that do not fit the requirements for inclusion in the RefSeq Curated or the RefSeq Predicted tracks. Examples are untranscribed pseudogenes or gene clusters, such as HOX or protocadherin alpha. They were manually curated from publications or databases but are not typical transcribed genes. RefSeq Alignments &ndash; alignments of RefSeq RNAs to the mouse genome provided by the RefSeq group, following the display conventions for PSL tracks. RefSeq Diffs &ndash; alignment differences between the mouse reference genome(s) and RefSeq curated transcripts. (Track not currently available for every assembly.) UCSC RefSeq &ndash; annotations generated from UCSC's realignment of RNAs with NM and NR accessions to the mouse genome. This track was previously known as the &quot;RefSeq Genes&quot; track. RefSeq Select (subset, only on hg38) &ndash; Subset of RefSeq Curated, transcripts marked as part of the RefSeq Select dataset. A single Select transcript is chosen as representative for each protein-coding gene. See NCBI RefSeq Select. RefSeq HGMD (subset) &ndash; Subset of RefSeq Curated, transcripts annotated by the Human Gene Mutation Database. This track is only available on the human genomes hg19 and hg38. It is the most restricted RefSeq subset, targeting clinical diagnostics. The RefSeq All, RefSeq Curated, RefSeq Predicted, and UCSC RefSeq tracks follow the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), or reviewed (dark), as defined by RefSeq. Color Level of review Reviewed: the RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information. Provisional: the RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association has been established by outside collaborators or NCBI staff. Predicted: the RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted. The item labels and codon display properties for features within this track can be configured through the check-box controls at the top of the track description page. To adjust the settings for an individual subtrack, click the wrench icon next to the track name in the subtrack list . Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name or OMIM identifier instead of the gene name, show all or a subset of these labels including the gene name, OMIM identifier and accession names, or turn off the label completely. Codon coloring: This track has an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. The RefSeq Diffs track contains five different types of inconsistency between the reference genome sequence and the RefSeq transcript sequences. The five types of differences are as follows: mismatch &ndash; aligned but mismatching bases, plus HGVS g. to show the genomic change required to match the transcript and HGVS c./n. to show the transcript change required to match the genome. short gap &ndash; genomic gaps that are too small to be introns (arbitrary cutoff of &lt; 45 bp), most likely insertions/deletion variants or errors, with HGVS g. and c./n. showing differences. shift gap &ndash; shortGap items whose placement could be shifted left and/or right on the genome due to repetitive sequence, with HGVS c./n. position range of ambiguous region in transcript. Here, thin and thick lines are used -- the thin line shows the span of the repetitive sequence, and the thick line shows the rightmost shifted gap. double gap &ndash; genomic gaps that are long enough to be introns but that skip over transcript sequence (invisible in default setting), with HGVS c./n. deletion. skipped &ndash; sequence at the beginning or end of a transcript that is not aligned to the genome (invisible in default setting), with HGVS c./n. deletion HGVS Terminology (Human Genome Variation Society): g. = genomic sequence ; c. = coding DNA sequence ; n. = non-coding RNA reference sequence. When reporting HGVS with RefSeq sequences, to make sure that results from research articles can be mapped to the genome unambiguously, please specify the RefSeq annotation release displayed on the transcript's Genome Browser details page and also the RefSeq transcript ID with version (e.g. NM_012309.4 not NM_012309). Methods Tracks contained in the RefSeq annotation and RefSeq RNA alignment tracks were created at UCSC using data from the NCBI RefSeq project. Data files were downloaded from RefSeq in GFF file format and converted to the genePred and PSL table formats for display in the Genome Browser. Information about the NCBI annotation pipeline can be found here. The RefSeq Diffs track is generated by UCSC using NCBI's RefSeq RNA alignments. The UCSC RefSeq Genes track is constructed using the same methods as previous RefSeq Genes tracks. RefSeq RNAs were aligned against the mouse genome using BLAT. Those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept. Data Access The raw data for these tracks can be accessed in multiple ways. It can be explored interactively using the REST API, Table Browser or Data Integrator. The tables can also be accessed programmatically through our public MySQL server or downloaded from our downloads server for local processing. The previous track versions are available in the archives of our downloads server. You can also access any RefSeq table entries in JSON format through our JSON API. The data in the RefSeq Other and RefSeq Diffs tracks are organized in bigBed file format; more information about accessing the information in this bigBed file can be found below. The other subtracks are associated with database tables as follows: genePred format: RefSeq All - ncbiRefSeq RefSeq Curated - ncbiRefSeqCurated RefSeq Predicted - ncbiRefSeqPredicted UCSC RefSeq - refGene PSL format: RefSeq Alignments - ncbiRefSeqPsl The first column of each of these tables is &quot;bin&quot;. This column is designed to speed up access for display in the Genome Browser, but can be safely ignored in downstream analysis. You can read more about the bin indexing system here. The annotations in the RefSeqOther and RefSeqDiffs tracks are stored in bigBed files, which can be obtained from our downloads server here, ncbiRefSeqOther.bb and ncbiRefSeqDiffs.bb. Individual regions or the whole set of genome-wide annotations can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system from the utilities directory linked below. For example, to extract only annotations in a given region, you could use the following command: bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/mm9/ncbiRefSeq/ncbiRefSeqOther.bb -chrom=chr16 -start=34990190 -end=36727467 stdout You can download a GTF format version of the RefSeq All table from the GTF downloads directory. The genePred format tracks can also be converted to GTF format using the genePredToGtf utility, available from the utilities directory on the UCSC downloads server. The utility can be run from the command line like so: genePredToGtf mm9 ncbiRefSeqPredicted ncbiRefSeqPredicted.gtf Note that using genePredToGtf in this manner accesses our public MySQL server, and you therefore must set up your hg.conf as described on the MySQL page linked near the beginning of the Data Access section. A file containing the RNA sequences in FASTA format for all items in the RefSeq All, RefSeq Curated, and RefSeq Predicted tracks can be found on our downloads server here. Please refer to our mailing list archives for questions. Previous versions of the ncbiRefSeq set of tracks can be found on our archive download server. Credits This track was produced at UCSC from data generated by scientists worldwide and curated by the NCBI RefSeq project. References Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 
refGene UCSC RefSeq UCSC annotations of RefSeq RNAs (NM_* and NR_*) Genes and Gene Predictions Description The RefSeq Genes track shows known mouse protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly. Please visit the Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark). The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely. Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box. Methods RefSeq RNAs were aligned against the mouse genome using BLAT. Those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project. References Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. PMID: 24259432; PMC: PMC3965018 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 
rmsk RepeatMasker Repeating Elements by RepeatMasker Variation and Repeats Description This track was created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. The program outputs a detailed annotation of the repeats that are present in the query sequence (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked (generally available on the Downloads page). RepeatMasker uses the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka (2000) in the References section below. Some newer assemblies have been made with Dfam, not Repbase. You can find the details for how we make our database data here in our &quot;makeDb/doc/&quot; directory. Display Conventions and Configuration In full display mode, this track displays up to ten different classes of repeats: Short interspersed nuclear elements (SINE), which include ALUs Long interspersed nuclear elements (LINE) Long terminal repeat elements (LTR), which include retroposons DNA repeat elements (DNA) Simple repeats (micro-satellites) Low complexity repeats Satellite repeats RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA) Other repeats, which includes class RC (Rolling Circle) Unknown The level of color shading in the graphical display reflects the amount of base mismatch, base deletion, and base insertion associated with a repeat element. The higher the combined number of these, the lighter the shading. A &quot;?&quot; at the end of the &quot;Family&quot; or &quot;Class&quot; (for example, DNA?) signifies that the curator was unsure of the classification. At some point in the future, either the &quot;?&quot; will be removed or the classification will be changed. Methods Data are generated using the RepeatMasker -s flag. Additional flags may be used for certain organisms. Repeats are soft-masked. Alignments may extend through repeats, but are not permitted to initiate in them. See the FAQ for more information. Credits Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track. References Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010. Repbase Update is described in: Jurka J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420. PMID: 10973072 For a discussion of repeats in mammalian genomes, see: Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):657-63. PMID: 10607616 Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846 
cpgIslandExtUnmasked Unmasked CpG CpG Islands on All Sequence (Islands < 300 Bases are Light Green) Expression and Regulation Description CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time, methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some other reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole. The unmasked version of the track displays potential CpG islands that exist in repeat regions and would otherwise not be visible in the repeat masked version. By default, only the masked version of the track is displayed. To view the unmasked version, change the visibility settings in the track controls at the top of this page. Methods CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. Each segment was then evaluated for the following criteria: GC content of 50% or greater length greater than 200 bp ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the number of Gs and Cs in the segment The entire genome sequence, masking areas included, was used for the construction of the track Unmasked CpG. The track CpG Islands is constructed on the sequence after all masked sequence is removed. The CpG count is the number of CG dinucleotides in the island. The Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length. The ratio of observed to expected CpG is calculated according to the formula (cited in Gardiner-Garden et al. (1987)): Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence. The calculation of the track data is performed by the following command sequence: twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \ | cpg_lh /dev/stdin 2&gt; cpg_lh.err \ | awk '{&dollar;2 = &dollar;2 - 1; width = &dollar;3 - &dollar;2; printf("%s\t%d\t%s\t%s %s\t%s\t%s\t%0.0f\t%0.1f\t%s\t%s\n", &dollar;1, &dollar;2, &dollar;3, &dollar;5, &dollar;6, width, &dollar;6, width*&dollar;7*0.01, 100.0*2*&dollar;6/width, &dollar;7, &dollar;9);}' \ | sort -k1,1 -k2,2n &gt; cpgIsland.bed The unmasked track data is constructed from twoBitToFa -noMask output for the twoBitToFa command. Data access CpG islands and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. All the tables can also be queried directly from our public MySQL servers, with more information available on our help page as well as on our blog. The source for the cpg_lh program can be obtained from src/utils/cpgIslandExt/. The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file") Credits This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished). References Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447 
blastHg18KG Human Proteins Human Proteins Mapped by Chained tBLASTn Genes and Gene Predictions Description This track contains tBLASTn alignments of the peptides from the predicted and known genes identified in the hg18 UCSC Genes track. Methods First, the predicted proteins from the human UCSC Genes track were aligned with the human genome using the Blat program to discover exon boundaries. Next, the amino acid sequences that make up each exon were aligned with the mouse sequence using the tBLASTn program. Finally, the putative mouse exons were chained together using an organism-specific maximum gap size but no gap penalty. The single best exon chains extending over more than 60% of the query protein were included. Exon chains that extended over 60% of the query and matched at least 60% of the protein's amino acids were also included. Credits tBLASTn is part of the NCBI BLAST tool set. For more information on BLAST, see Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-410. Blat was written by Jim Kent. The remaining utilities used to produce this track were written by Jim Kent or Brian Raney. 
xenoRefGene Other RefSeq Non-Mouse RefSeq Genes Genes and Gene Predictions Description This track shows known protein-coding and non-protein-coding genes for organisms other than mouse, taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated weekly. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), reviewed (dark). The item labels and display colors of features within this track can be configured through the controls at the top of the track description page. Label: By default, items are labeled by gene name. Click the appropriate Label option to display the accession name instead of the gene name, show both the gene and accession names, or turn off the label completely. Codon coloring: This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. Click here for more information about this feature. Hide non-coding genes: By default, both the protein-coding and non-protein-coding genes are displayed. If you wish to see only the coding genes, click this box. Methods The RNAs were aligned against the mouse genome using blat; those with an alignment of less than 15% were discarded. At least 40 bases must be aligned to DNA that is not repeat masked. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 1.0% of the best and at least 35% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project. References Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
acembly AceView Genes AceView Gene Models With Alt-Splicing Genes and Gene Predictions Description This track shows AceView gene models constructed from cDNA and genomic evidence by Danielle and Jean Thierry-Mieg using the Acembly program. AceView is the only database that defines the genes genome-wide by using only, but exhaustively, the public experimental cDNA sequences from the same species. The analysis relies on the quality of the genome sequence and exploits sophisticated cDNA-to-genome co-alignment algorithms to provide a comprehensive and non-redundant representation of the GenBank, dbEST, GSS, Trace and RefSeq cDNA sequences. In a way, the AceView transcripts represent a fully annotated non-redundant &lsquo;nr&rsquo; view of the public RNAs, minus cloning artefacts, contaminations and bad quality sequences. AceView transcripts represent a 10 times compaction relative to the raw data, with minimal loss of sequence information. 87% of the public RNA sequences are coalesced into AceView alternative transcripts and genes, thereby identifying close to twice as many main genes as there are &quot;known genes&quot; in both human and mouse. 18% to 25% of the spliced genes appear non-coding, in mouse and human respectively. Alternative transcripts are prominent in both species. The typical human gene produces on average eight distinct alternatively spliced forms from three promoters and with three non-overlapping terminal exons. It has on average three cassette exons and four internal donor or acceptor sites. The AceView site further proposes a thorough biological annotation of the reconstructed genes, including association to diseases and tissue specificity of the alternative transcripts. AceView combines respect for the experimental data with extensive quality control. Evaluated in the ENCODE regions, AceView transcripts are close to indistinguishable from the manually curated Gencode reference genes (see Thierry-Mieg, 2006, or compare the two tracks in the Genome Browser), but over the entire genome the number of transcripts exceeds Havana/Vega by a factor of three and RefSeq by a factor of six. Display Conventions and Configuration This track follows the display conventions for gene tracks. Gene models that fall into the &quot;main&quot; class are displayed in purple; &quot;putative&quot; genes are displayed in pink. The main genes include at least one transcript which is spliced or putatively protein coding. Spliced genes contain at least one well-defined standard intron, i.e., an intron with a GT-AG or GC-AG boundary, supported by at least one clone matching exactly, with no ambiguous bases, 8 bases of the genome on each side of the intron. The putative genes have no standard intron and do not encode good proteins, yet are supported by more than six cDNA clones. The track description page offers the following filter and configuration options: Gene Class filter: Select the main or putative option to filter the display. Color track by codons: Select the genomic codons option to color and label each codon in a zoomed-in display to facilitate validation and comparison to gene predictions. Click the Codon coloring help link on the track description page for more information about this feature. Methods The millions of cDNA sequences available from the public databases (GenBank, dbEST, GSS, Traces, etc.) are aligned cooperatively on the genome sequence, taking care to keep the paired 5' and 3' reads from single clones associated in the same transcript. Useful information about tissue, stage, publications, isolation procedure and so on is gathered. AceView alignments on the genome use knowledge on sequencing errors gained from analyzing sequencing traces and cooperative refinements. They are usually obtained over the entire length of the EST or mRNA, (average 98.8% aligned, 0.2% mismatches in mRNAs or 95.5% aligned, 1.4% mismatches in ESTs). Multiple alignments are evaluated and the sequences are stringently kept only in their best position genome-wide. Less than 1% of the mRNAs and less than 2% of the ESTs will ultimately be aligned in more than one gene, usually in the ~1% closely repeated genes. The cDNA sequences are then processed and cleaned: the vectors and polyA are clipped, the reads submitted on the wrong strand are flipped, and the small insertion or deletion polymorphisms are identified. Eventual cDNA clone rearrangements or anomalous alignments are flagged and filtered (akin to manually) so as not to lose unique valuable information while avoiding pollution of the database with poorly supported anomalous data. Unfortunately, cDNA libraries are still far from saturation, so after 20% of the suspicious entries have been removed, a single good-quality cDNA sequence, aligned with standard introns on the genome, is considered sufficient evidence for a given mRNA structure. That is because cDNA sequences are difficult to obtain, but they remain the cleanest and most reliable information to best define the molecular genes. Unspliced non-coding genes are however reported (in the putative class) only if they are supported by six or more accessions. Others belong to what is termed &lsquo;the cloud&rsquo; (not displayed on the UCSC Genome Browser). The cDNA sequences are clustered into a minimal number of alternative transcript variants, preferring partial transcripts to artificially extended ones. Sequences are concatenated by simple contact, but the combinatorics are voided by allowing each cDNA accession to contribute to a single alternative variant, preferably one where it merges silently without bringing any new sequence information. As a result, for instance, all shorter reads compatible with a full-length mRNA will be absorbed in that transcript and will not be available to allow for extensions on other incompatible transcripts. About 70% of the variants, clearly identified on the Acembly site, have their entire coding region supported by a single cDNA; the others may be illicit concatenations that could be split when more data become available. For each transcript, the consensus sequence of the cDNAs most compatible to the genome sequence is generated. Single base insertion, deletion, transition or transversion is shown graphically in the mRNA view, where frequent SNPs become evident. The main sequence of the transcript used in the annotation is that of the footprint of the transcript on the genome, which is of better quality than the mRNAs: this procedure corrects up to 2% sequencing errors. Putative protein-coding regions are predicted from the mRNA sequence and annotated using BlastP, PFAM, Psort2, and comparison to AceView proteins from other species. Best proteins are scored (see the FAQ on the Acembly site) and transcripts are putatively proposed to be protein-coding or non-coding. Expression, cDNA support, tissue specificity, sequences of alternative transcripts, introns and exons, alternative promoters, alternative exons and alternative polyadenylation sites are evaluated and annotated on the Acembly web site. The reconstructed alternative transcripts are then grouped into genes if they share at least one exact intron boundary or if they have substantial sequence overlap. Coding and non-coding genes are defined, and genes in antisense are flagged. AceView genes are matched molecularly to Entrez genes and named according to the official nomenclature or the Entrez Gene nomenclature. For novel genes not in Entrez, AceView creates new gene names that are maintained from release to release until the genes receive an official or Entrez gene name. Each gene is annotated in depth, with the intention of AceView serving as a one-stop knowledgebase for systems biology. Selected functional annotations are gathered from various sources, including expression data, protein interactions and GO annotations. In particular, possible disease associations are extracted directly from PubMed, in addition to OMIM and GAD, and the users can help refine those annotations. Finally, lists of the most closely related genes by function, pathway, protein complex, GO annotation, disease, cellular localization or all criteria taken together are proposed, to stimulate research and development. Click the &quot;AceView Gene Summary&quot; on an individual transcript's details page to access the gene on the NCBI AceView website. Credits Thanks to Danielle and Jean Thierry-Mieg at NCBI for providing this track for human, worm and mouse. References Thierry-Mieg D, Thierry-Mieg J. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 2006;7 Suppl 1:S12.1-14. PMID: 16925834; PMC: PMC1810549 AceView web site: https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly 
affyAllExonProbes Affy Exon Probes Affymetrix Exon Array 1.0: Probesets Expression and Regulation Description The Exon GeneChip contains over one million probe sets designed to interrogate individual exons rather than the 3' ends of transcripts as in traditional GeneChips. Exons were derived from a variety of annotations that have been divided into the classes Core, Extended and Full. Core: RefSeq transcripts, full-length GenBank mRNAs Extended: dbEst alignments, Ensembl annotations, syntenic mRNA from human, rat and mouse, microRNA annotations, MITOMAP annotations, Vega genes, Vega pseudogenes Full: Geneid genes, Genscan genes, Genscan Subopt, Exoniphy, RNA genes, SGP genes, Twinscan genes Probe sets are colored by class with the Core probe sets being the darkest and the Full being the lightest color. Additionally, probe sets that do not overlap the exons of a transcript cluster, but fall inside of its introns, are considered bounded by that transcript cluster and are colored slightly lighter. Probe sets that overlap the coding portion of the Core class are colored slightly darker. The microarray track using this probe set can be displayed by turning on the Affy Exon Tissue track. Credits and References The exons interrogated by the probe sets displayed in this track are from the Affymetrix Exon 1.0 GeneChip and were derived from a number of sources. In addition to the millions of cDNA sequences contributed to the GenBank, dbEst and RefSeq databases by individual labs and scientists, the following annotations were used: Ensembl: Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41. PMID: 11752248; PMC: PMC99161 Exoniphy: Siepel, A., Haussler, D. Computational identification of evolutionarily conserved exons. Proc. 8th Int'l Conf. on Research in Computational Molecular Biology, 177-186 (2004). Geneid Genes: Parra G, Blanco E, Guig&#243; R. GeneID in Drosophila. Genome Res. 2000 Apr;10(4):511-5. PMID: 10779490; PMC: PMC310871 Genscan Genes: Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997 Apr 25;268(1):78-94. PMID: 9149143 microRNA: Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11. PMID: 14681370; PMC: PMC308757 MITOMAP: Kogelnik AM, Lott MT, Brown MD, Navathe SB, Wallace DC. MITOMAP: a human mitochondrial genome database. Nucleic Acids Res. 1996 Jan 1;24(1):177-9. PMID: 8594574; PMC: PMC145607 RNA Genes: Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997 Mar 1;25(5):955-64. PMID: 9023104; PMC: PMC146525 SGP Genes: Wiehe T, Gebauer-Jung S, Mitchell-Olds T, Guig&#243; R. SGP-1: prediction and validation of homologous genes based on sequence alignments. Genome Res. 2001 Sep;11(9):1574-83. PMID: 11544202; PMC: PMC311140 Twinscan Genes: Korf I, Flicek P, Duan D, Brent MR. Integrating genomic homology into gene structure prediction. Bioinformatics. 2001;17 Suppl 1:S140-8. PMID: 11473003 Vega Genes and Pseudogenes: The HAVANA group, Wellcome Trust Sanger Institute. 
affyAllExonSuper Affy Exon Affymetrix All Exon Microarrays Expression and Regulation Overview This super-track combines related tracks of the Affymetrix All Exon chip data. There are two member tracks: Affymetrix Exon Array 1.0: Normal Tissues: This track displays data from 11 different sample tissues across three replicate arrays each. Affymetrix Exon Array 1.0: Probesets: This track displays probeset loci for the array. 
affyExonTissues Affy Exon Tissues Affymetrix Exon Array 1.0: Normal Tissues Expression and Regulation Methods RNA (from a commercial source) from 11 tissues were hybridized to Affymetrix Mouse Exon 1.0 ST arrays. For each tissue, 3 replicate experiments were performed for a total of 33 arrays. The raw intensity signal from the arrays was normalized with a quantile normalization method, then run through the PLIER algorithm. The normalized data were then converted to median-centered log-ratios, which are displayed as green for negative log-ratios (below-median expression), and red for positive (above-median expression). The probe sets for this microarray track are shown in the the Affy Exon Probes track. Credits This track was produced by Andy Pohl, Kayla Smith, and Pauline Fujita of the genome browser group at UCSC, Melissa Cline of the Ares lab at UCSC, and Chuck Sugnet at Affymetrix, based on sample exon array data available from Affymetrix, produced by Tyson Clark. References Pohl AA, Sugnet CW, Clark TA, Smith K, Fujita PA, Cline MS. Affy exon tissues: exon levels in normal tissues in human, mouse and rat. Bioinformatics. 2009 Sep 15;25(18):2442-3. PMID: 19570805; PMC: PMC2735668 Links Affymetrix Mouse Exon 1.0 ST array web page Affymetrix Mouse Exon data PLIER algorithm documentation (PDF). 
affyGnf1m Affy GNF1M Alignments of Probes from Affymetrix GNF1M Chip Expression and Regulation Description This track shows the location of the sequences used for the selection of probes on the Affymetrix GNF1M chips. The annotation contains 31,000 non-overlapping mouse genes and gene predictions. Methods The sequences were mapped to the genome with blat followed by pslReps using the parameters -minCover=0.3, -minAli=0.95 and -nearTop=0.005. Credits Thanks to the Genomics Institute of the Novartis Research Foundation (GNF) for the data underlying this track. 
affyMOE430 Affy MOE430 Alignments of Affymetrix Consensus Sequences from Mouse MOE430 (A and B) Expression and Regulation Description This track shows the location of the consensus sequences used for the selection of probes on the Affymetrix Mouse MOE430 set (A and B) of chips. Methods Consensus sequences were downloaded from the Affymetrix Product Support and mapped to the genome with blat followed by pslReps using the parameters -minCover=0.3, -minAli=0.95 and -nearTop=0.005. Credits Thanks to Affymetrix for the data underlying this track. 
affyU74 Affy U74 Alignments of Affymetrix Consensus Sequences from MG-U74 v2 (A,B, and C) Expression and Regulation Description This track shows the location of the consensus sequences used for the selection of probes on the Affymetrix MG-U74v2 set (A,B and C) of chips. Methods Consensus sequences were downloaded from the Affymetrix Product Support and mapped to the genome with blat followed by pslReps using the parameters -minCover=0.3, -minAli=0.95 and -nearTop=0.005. Credits Thanks to Affymetrix for the data underlying this track. 
genotypeArrays Agilent CGH Agilent CGH Microarray probesets Variation and Repeats Description This track displays the probes from the Agilent Catalog Oligonucleotide Microarrays. Agilent's oligonucleotide CGH (Comparative Genomic Hybridization) platform enables the study of genome-wide DNA copy number changes at a high resolution. The probes on Agilent aCGH microarrays are 60-mer oligonucleotides synthesized in situ using Agilent's inkjet SurePrint technology. The probes represented on the Agilent CGH microarrays have been selected using algorithms developed specifically for the CGH application, assuring optimal performance of these probes in detecting DNA copy number changes. The Agilent catalog CGH microarrays are printed on 1 in. x 3 in. glass slides and are available in several formats. The mouse catalog SurePrint G3 microarrays formats are the 1x1M and 4x180K. The legacy mouse catalog SurePrint HD microarrays are the 1x244K and 2x105K. Subtracks were colored in alternating shades of green and orange to highlight track boundaries. This track consists of the following subtracks: Description AMADID Samples per Slide Biological Features Median Probe Spacing Gene-biased SurePrint G3 Mouse CGH Microarray 1x1M 027414 1 967,265 1.8 kb Yes SurePrint G3 Mouse CGH Microarray 4x180K 027411 4 174,307 11 kb Yes SurePrint HD Mouse CGH Microarray 1x244K 014695 1 235,188 7.8 kb Yes SurePrint HD Mouse CGH Microarray 2x105K 014699 2 98,510 19 kb Yes References More information on the Agilent Oligonucleotide Microarrays is available here. Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R, Tsang P, Curry B, Baird K, Meltzer PS et al. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17765-70. PMID: 15591353; PMC: PMC535426 Credits Thanks to Shane Giles, Peter Webb, and Anniek De Witte from Agilent Technologies for providing these data. 
agilentCgh105a Ag CGH 2x105K Agilent SurePrint HD Mouse CGH Microarray 2x105K AMADID 014699 Variation and Repeats 
agilentCgh244a Ag CGH 1x244K Agilent SurePrint HD Mouse CGH Microarray 1x244K AMADID 014695 Variation and Repeats 
agilentCgh4x180k Ag CGH 4x180K Agilent SurePrint G3 Mouse CGH Microarray 4x180K AMADID 027411 Variation and Repeats 
agilentCgh1x1m Ag CGH 1x1M Agilent SurePrint G3 Mouse CGH Microarray 1x1M AMADID 027414 Variation and Repeats 
allenBrainAli Allen Brain Allen Brain Atlas Probes Expression and Regulation Description This track provides a link into the Allen Brain Atlas (ABA) images for this probe. The ABA is an extensive database of high resolution in-situ hybridization images of adult male mouse brains covering the majority of genes. Methods The ABA created a platform for high-throughput in situ hybridization (ISH) that allows a highly systematic approach to analyzing gene expression in the brain. ISH is a technique that allows the cellular localization of mRNA transcripts for specific genes. Labeled antisense probes, specific to a particular gene, are hybridized to cellular (sense) transcripts and subsequent detection of the bound probe produces specific labeling in those cells expressing the particular gene. This method involves tagged nucleotides detected by colorimetric methods. The platform used for the ABA utilizes this non-isotopic approach, with digoxigenin-labeled nucleotides incorporated into a riboprobe produced by in vitro transcription. This method produces a label that fills the cell body, in contrast to autoradiography that produces scattered silver grains surrounding each labeled cell. To enhance the ability to detect low level expression, the ABA has incorporated a tyramide signal amplification step into the protocol that greatly increases sensitivity. The specific methodology is described in detail within the ABA Data Production Processes document. Credits Thanks to the Allen Institute for Brain Science in general, and Susan Sunkin in particular, for coordinating with UCSC on this annotation. 
gold Assembly Assembly from Fragments Mapping and Sequencing Description This track shows the draft assembly of the mouse genome. Whole-genome shotgun reads were assembled into contigs. When possible, contigs were grouped into scaffolds (also known as &quot;supercontigs&quot;). The order, orientation and gap sizes between contigs within a scaffold are based on paired-end read evidence. In dense mode, this track depicts the contigs that make up the currently viewed scaffold. Contig boundaries are distinguished by the use of alternating gold and brown coloration. Where gaps exist between contigs, spaces are shown between the gold and brown blocks. The relative order and orientation of the contigs within a scaffold is always known; therefore, a line is drawn in the graphical display to bridge the blocks. Clone Type Key: W - Whole Genome Shotgun contig F - Finished A - In Active Finishing D - Draft 
augustusGene AUGUSTUS AUGUSTUS ab initio gene predictions v3.1 Genes and Gene Predictions Description This track shows ab initio predictions from the program AUGUSTUS (version 3.1). The predictions are based on the genome sequence alone. For more information on the different gene tracks, see our Genes FAQ. Methods Statistical signal models were built for splice sites, branch-point patterns, translation start sites, and the poly-A signal. Furthermore, models were built for the sequence content of protein-coding and non-coding regions as well as for the length distributions of different exon and intron types. Detailed descriptions of most of these different models can be found in Mario Stanke's dissertation. This track shows the most likely gene structure according to a Semi-Markov Conditional Random Field model. Alternative splicing transcripts were obtained with a sampling algorithm (--alternatives-from-sampling=true --sample=100 --minexonintronprob=0.2 --minmeanexonintronprob=0.5 --maxtracks=3 --temperature=2). The different models used by Augustus were trained on a number of different species-specific gene sets, which included 1000-2000 training gene structures. The --species option allows one to choose the species used for training the models. Different training species were used for the --species option when generating these predictions for different groups of assemblies. Assembly Group Training Species Fish zebrafish Birds chicken Human and all other vertebrates human Nematodes caenorhabditis Drosophila fly A. mellifera honeybee1 A. gambiae culex S. cerevisiae saccharomyces This table describes which training species was used for a particular group of assemblies. When available, the closest related training species was used. Credits Thanks to the Stanke lab for providing the AUGUSTUS program. The training for the chicken version was done by Stefanie K&ouml;nig and the training for the human and zebrafish versions was done by Mario Stanke. References Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656 Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25. PMID: 14534192 
bacEndPairs BAC End Pairs BAC End Pairs Mapping and Sequencing Description Bacterial artificial chromosomes (BACs) are a key part of many large scale sequencing projects. A BAC typically consists of 25 - 350 kb of DNA. During the early phase of a sequencing project, it is common to sequence a single read (approximately 500 bases) off each end of a large number of BACs. Later on in the project, these BAC end reads can be mapped to the genome sequence. This track shows these mappings in cases where both ends could be mapped. These BAC end pairs can be useful for validating the assembly over relatively long ranges. In some cases, the BACs are useful biological reagents. This track can also be used for determining which BAC contains a given gene, useful information for certain wet lab experiments. A valid pair of BAC end sequences must be at least 25 kb but no more than 350 kb away from each other. The orientation of the first BAC end sequence must be &quot;+&quot; and the orientation of the second BAC end sequence must be &quot;-&quot;. The scoring scheme used for this annotation assigns 1000 to an alignment when the BAC end pair aligns to only one location in the genome (after filtering). When a BAC end pair or clone aligns to multiple locations, the score is calculated as 1500/(number of alignments). Methods BAC end sequences are placed on the assembled sequence using Jim Kent's blat program. Credits Additional information about the clone, including how it can be obtained, may be found at the NCBI Clone Registry. To view the registry entry for a specific clone, open the details page for the clone and click on its name at the top of the page. 
wgEncodeCaltechHist Caltech Histone GSE36023 Histone Modifications by ChIP-seq from ENCODE/Caltech Expression and Regulation Description Rationale for the Mouse ENCODE project Our knowledge of the function of genomic DNA sequences comes from three basic approaches. Genetics uses changes in behavior or structure of a cell or organism in response to changes in DNA sequence to infer function of the altered sequence. Biochemical approaches monitor states of histone modification, binding of specific transcription factors, accessibility to DNases and other epigenetic features along genomic DNA. In general, these are associated with gene activity, but the precise relationships remain to be established. The third approach is evolutionary, using comparisons among homologous DNA sequences to find segments that are evolving more slowly or more rapidly than expected given the local rate of neutral change. These are inferred to be under negative or positive selection, respectively, and we interpret these as DNA sequences needed for a preserved (negative selection) or adaptive (positive selection) function. The ENCODE project aims to discover all the DNA sequences associated with various epigenetic features, with the reasonable expectation that these will also be functional (best tested by genetic methods). However, it is not clear how to relate these results with those from evolutionary analyses. The mouse ENCODE project aims to make this connection explicitly and with a moderate breadth. Assays identical to those being used in the ENCODE project are performed in cell types in mouse that are similar or homologous to those studied in the human project. Thus, we will be able to discover which epigenetic features are conserved between mouse and human, and we can examine the extent to which these overlap with the DNA sequences under negative selection. The contribution of DNA that with a function preserved in mammals versus that with a function in only one species will be discovered. The results will have a significant impact on our understanding of the evolution of gene regulation. Maps of Occupancy by Transcription Factors Genome-wide occupancy maps of transcription factors (TFs) are generated by ChIP-seq. A ChIP-Seq experiment combines a chromatin immunoprecipitation (ChIP) experiment that enriches genomic DNA for the segments bound by specific proteins (the antigens recognized by the antibody) with high-throughput short read sequencing of the enriched DNA fragments (Wold & Myers, 2008). Proteins are crosslinked to DNA (usually with formaldehyde), chromatin is sheared and immunoprecipitated with the antibody of interest. The immunoprecipitated material is turned into a sequencing library and sequenced. The sequencing reads are then aligned to the genome. A control sample consisting of sonicated chromatin that has not been immunoprecipitated or immunoprecipitated with a non-specific immunoglobulin is also sequenced. The ChIP and the control datasets are analyzed with a variety of software packages to identify regions occupied by the target protein. The sequencing data, alignments and analysis files for 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. This track contains the following views: Peaks Regions of signal enrichment based on processed data. Intensity is represented in grayscale, the darker shading shows higher intensity (a solid vertical line in the peak region represents the point with the highest signal). Signal Density graph (wiggle) of signal enrichment based on processed data of all mapped read intensity of the signal is represented as RPM (Read 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. Chromatin immunoprecipitation followed published methods (Johnson & Mortazavi et al., 2007) with the exception of certain experiments for which glutaraldehyde was added to the crosslink reaction. Information on the antibodies used is available via the metadata for each subtrack. Libraries were constructed using the Illumina ChIP-seq Sample Preparation Kit or using a modified protocol that includes the addition of multiplexing tags to the fragments. DNA fragments were repaired to generate blunt ends and a single A nucleotide was added to each end. Double-stranded Illumina adaptors or Double-stranded Illumina adaptors with multiplexing tags were ligated to the fragments. Ligation products were amplified by 18 cycles of PCR, and the DNA between 150-250 bp was gel purified. Completed libraries were quantified with Quant-iT dsDNA HS Assay Kit. The DNA library was sequenced on the Illumina GAII and GAIIx sequencing systems, and more recently, for multiplexed libraries, several of them were pooled and sequenced on the HiSeq platform. Cluster generation, linearization, blocking and sequencing primer reagents were provided in the Illumina Cluster Amplification kits. Older libraries were generated using 2 rounds of PCR. Matched input samples were sequenced for each variation of fixation conditions and the number of PCR rounds. Reads of 32 bp, 36 bp or 50 bp length were generated. Sequencing reads (fastq files) were assigned to the corresponding libraries based on the multiplexing tag for pooled libraries (all tags have been removed from reads in the fastq files available for download) or directly processed. Bowtie (Langmead et al., 2009) was used to map reads to the male or female version of the mouse genome (excluding the _random chromosomes in the assembly) depending on the cell line sex. The following parameters were used: "-v 2 -k 11 -m 10 -t --best --strata". Aligned reads were converted into rds files using the ERANGE package (Johnson & Mortazavi et al., 2007) and the findall.py program in ERANGE was used to identify enriched regions against the matching input sample. The following settings were used for point-source transcription factors: "--shift learn --ratio 3 --minimum 2 --listPeak --revbackground". For histone modifications, the settings were changed to "--notrim --nodirectionality --spacing 100 --ratio 3 --minimum 2 --listPeak --revbackground". Credits Cell growth, ChIP, and Illumina library construction were done in the laboratory of Barbara Wold, (California Institute of Technology). Sequencing was done at the Millard and Muriel Jacobs Genetics and Genomics Laboratory at the California Institute of Technology, initial HiSeq data was generated at Illumina Inc., Hawyard, CA. Cell growth and ChIP: Georgi Marinov, Katherine Fisher, Gordon Kwan, Antony Kirilusha, Ali Mortazavi, Gilberto DeSalvo, Brian Williams Library Construction, Sequencing and Primary Data Handling: Lorianne Schaeffer, Diane Trout , Igor Antoschechkin (California Institute of Technology), Lu Zhang, Gary Schroth (Illumina Inc.) Data Processing and Submission: Georgi Marinov, Diane Trout Contact: Barbara Wold, Georgi K. Marinov, Diane Trout 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. 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. Wold B, Myers RM. Sequence census methods for functional genomics. Nat Methods. 2008 Jan;5(1):19-21. 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. 
wgEncodeCaltechHistViewSignal Signal Histone Modifications by ChIP-seq from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12InputFCntrl50bPcr1xSigRep1 C2 Con 50bp 1 immortalized Input C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEM002113 2113 GSM918421 Hardison Caltech-m 11612 Myoblast PCR1x 1 input F C3H wgEncodeCaltechHistC2c12InputFCntrl50bPcr1xSigRep1 None Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 Contr 50bp Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12InputFCntrl50bE2p60hPcr1xSigRep1 C2 Con 50bp 60h 1 immortalized Input C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEM002126 2126 GSM918407 Hardison Caltech-m 11610 Myocyte PCR1x 1 input F C3H wgEncodeCaltechHistC2c12InputFCntrl50bE2p60hPcr1xSigRep1 EqS_2.0pct_60hr Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Contr 50bp Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12InputFCntrl32bPcr2xSigRep1 C2 Con 32bp 1 immortalized Input C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEM002111 2111 GSM918419 Hardison Caltech-m 10135 Myoblast PCR2x 1 input F C3H wgEncodeCaltechHistC2c12InputFCntrl32bPcr2xSigRep1 None Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 Contr 32bp Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12InputFCntrl32bE2p60hPcr2xSigRep1 C2 Con 32bp 60h 1 immortalized Input C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEM002112 2112 GSM918420 Hardison Caltech-m 10194 Myocyte PCR2x 1 input F C3H wgEncodeCaltechHistC2c12InputFCntrl32bE2p60hPcr2xSigRep1 EqS_2.0pct_60hr Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Contr 32bp Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12InputFCntrl32bE2p24hPcr2xSigRep1 C2 Con 32bp 24h 1 immortalized Input C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEM002110 2110 GSM918418 Hardison Caltech-m 10007 Myocyte PCR2x 1 input F C3H wgEncodeCaltechHistC2c12InputFCntrl32bE2p24hPcr2xSigRep1 EqS_2.0pct_24hr Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 24 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Contr 32bp Myocyte 24h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3k36me3FCntrl50bPcr1xSigRep1 C2 H3K36me3 1 immortalized H3K36me3 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEM002140 2140 GSM918417 Hardison Caltech-m 11905 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12H3k36me3FCntrl50bPcr1xSigRep1 None Signal Immortal cells Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 H3K36me3 Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3k36me3FCntrl50bE2p60hPcr1xSigRep1 C2 H3K36me3 60h 1 immortalized H3K36me3 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEM002139 2139 GSM918409 Hardison Caltech-m 11697 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12H3k36me3FCntrl50bE2p60hPcr1xSigRep1 EqS_2.0pct_60hr Signal Immortal cells Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 H3K36me3 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3k27me3FCntrl32bPcr2xSigRep1 C2 H3K27me3 1 immortalized H3K27me3 C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEM002138 2138 GSM918408 Hardison Caltech-m 10502 Myoblast PCR2x 1 exp F C3H wgEncodeCaltechHistC2c12H3k27me3FCntrl32bPcr2xSigRep1 None Signal Immortal cells 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. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 H3K27me3 Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3k27me3FCntrl32bE2p60hPcr2xSigRep1 C2 H3K27me3 60h 1 immortalized H3K27me3 C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-10 wgEncodeEM002143 2143 GSM918414 Hardison Caltech-m 10536 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechHistC2c12H3k27me3FCntrl32bE2p60hPcr2xSigRep1 EqS_2.0pct_60hr Signal Immortal cells 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. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 H3K27me3 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3k04me3FCntrl50bPcr1xSigRep1 C2 H3K4me3 1 immortalized H3K4me3 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEM002142 2142 GSM918415 Hardison Caltech-m 11956 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12H3k04me3FCntrl50bPcr1xSigRep1 None Signal Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 H3K4me3 Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3k04me3FCntrl50bE2p60hPcr1xSigRep1 C2 H3K4me3 60h 1 immortalized H3K4me3 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEM002141 2141 GSM918416 Hardison Caltech-m 11957 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12H3k04me3FCntrl50bE2p60hPcr1xSigRep1 EqS_2.0pct_60hr Signal Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 H3K4me3 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3ac06599FCntrl32bPcr2xSigRep1 C2 H3ac 1 immortalized H3ac_(06-599) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002149 2149 GSM918422 Hardison Caltech-m 10331 Myoblast PCR2x 1 exp F C3H wgEncodeCaltechHistC2c12H3ac06599FCntrl32bPcr2xSigRep1 None Signal Immortal cells missing Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 H3ac Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3ac06599FCntrl32bE2p24hPcr2xSigRep1 C2 H3ac 24h 1 immortalized H3ac_(06-599) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002148 2148 GSM918423 Hardison Caltech-m 10330 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechHistC2c12H3ac06599FCntrl32bE2p24hPcr2xSigRep1 EqS_2.0pct_24hr Signal Immortal cells missing Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 24 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 H3ac Myocyte 24h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12Ab3594FCntrl50bPcr1xSigRep1 C2 H3K79me2 1 immortalized H3K79me2_(ab3594) C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002146 2146 GSM918411 Hardison Caltech-m 11906 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12Ab3594FCntrl50bPcr1xSigRep1 None Signal Immortal cells H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 H3K79me2 Myoblast Histome Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12Ab3594FCntrl50bE2p60hPcr1xSigRep1 C2 H3K79me2 60h 1 immortalized H3K79me2_(ab3594) C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002145 2145 GSM918412 Hardison Caltech-m 11669 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12Ab3594FCntrl50bE2p60hPcr1xSigRep1 EqS_2.0pct_60hr Signal Immortal cells H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 H3K79me2 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12Ab32356FCntrl50bE2p60hPcr1xSigRep1 C2 H3K4me2 60h 1 immortalized H3K4me2_(ab32356) C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002144 2144 GSM918413 Hardison Caltech-m 11832 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12Ab32356FCntrl50bE2p60hPcr1xSigRep1 EqS_2.0pct_60hr Signal Immortal cells Histone H3 dimethylated on Lysine 4. Marks promoters and enhancers. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 H3K4me2 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12Ab2621FCntrl50bPcr1xSigRep1 C2 H3K79me3 1 immortalized H3K79me3_(ab2621) C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002147 2147 GSM918410 Hardison Caltech-m 11907 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12Ab2621FCntrl50bPcr1xSigRep1 None Signal Immortal cells Associated with the gene body of actively transcribed genes Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 H379me3 Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistViewPeaks Peaks Histone Modifications by ChIP-seq from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3k36me3FCntrl50bPcr1xPkRep1 C2 H3K36me3 1 immortalized H3K36me3 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEM002140 2140 GSM918417 Hardison Caltech-m 11905 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12H3k36me3FCntrl50bPcr1xPkRep1 None Peaks Immortal cells Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 H3K36me3 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3k36me3FCntrl50bE2p60hPcr1xPkRep1 C2 H3K36me3 60h 1 immortalized H3K36me3 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEM002139 2139 GSM918409 Hardison Caltech-m 11697 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12H3k36me3FCntrl50bE2p60hPcr1xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 H3K36me3 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3k27me3FCntrl32bPcr2xPkRep1 C2 H3K27me3 1 immortalized H3K27me3 C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEM002138 2138 GSM918408 Hardison Caltech-m 10502 Myoblast PCR2x 1 exp F C3H wgEncodeCaltechHistC2c12H3k27me3FCntrl32bPcr2xPkRep1 None Peaks Immortal cells 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. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 H3K27me3 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3k27me3FCntrl32bE2p60hPcr2xPkRep1 C2 H3K27me3 60h 1 immortalized H3K27me3 C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-10 wgEncodeEM002143 2143 GSM918414 Hardison Caltech-m 10536 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechHistC2c12H3k27me3FCntrl32bE2p60hPcr2xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells 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. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 H3K27me3 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3k04me3FCntrl50bPcr1xPkRep1 C2 H3K4me3 1 immortalized H3K4me3 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEM002142 2142 GSM918415 Hardison Caltech-m 11956 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12H3k04me3FCntrl50bPcr1xPkRep1 None Peaks Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 H3K4me3 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3k04me3FCntrl50bE2p60hPcr1xPkRep1 C2 H3K4me3 60h 1 immortalized H3K4me3 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-10 2012-05-10 wgEncodeEM002141 2141 GSM918416 Hardison Caltech-m 11957 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12H3k04me3FCntrl50bE2p60hPcr1xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 H3K4me3 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3ac06599FCntrl32bPcr2xPkRep1 C2 H3ac 1 immortalized H3ac_(06-599) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002149 2149 GSM918422 Hardison Caltech-m 10331 Myoblast PCR2x 1 exp F C3H wgEncodeCaltechHistC2c12H3ac06599FCntrl32bPcr2xPkRep1 None Peaks Immortal cells missing Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 H3ac Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12H3ac06599FCntrl32bE2p24hPcr2xPkRep1 C2 H3ac 24h 1 immortalized H3ac_(06-599) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002148 2148 GSM918423 Hardison Caltech-m 10330 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechHistC2c12H3ac06599FCntrl32bE2p24hPcr2xPkRep1 EqS_2.0pct_24hr Peaks Immortal cells missing Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 24 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 H3ac Myocyte 24h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12Ab3594FCntrl50bPcr1xPkRep1 C2 H3K79me2 1 immortalized H3K79me2_(ab3594) C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002146 2146 GSM918411 Hardison Caltech-m 11906 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12Ab3594FCntrl50bPcr1xPkRep1 None Peaks Immortal cells H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 H3K79me2 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12Ab3594FCntrl50bE2p60hPcr1xPkRep1 C2 H3K79me2 60h 1 immortalized H3K79me2_(ab3594) C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002145 2145 GSM918412 Hardison Caltech-m 11669 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12Ab3594FCntrl50bE2p60hPcr1xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 H3K79me2 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12Ab32356FCntrl50bE2p60hPcr1xPkRep1 C2 H3K4me2 60h 1 immortalized H3K4me2_(ab32356) C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002144 2144 GSM918413 Hardison Caltech-m 11832 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12Ab32356FCntrl50bE2p60hPcr1xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells Histone H3 dimethylated on Lysine 4. Marks promoters and enhancers. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 H3K4me2 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechHistC2c12Ab2621FCntrl50bPcr1xPkRep1 C2 H3K79me3 1 immortalized H3K79me3_(ab2621) C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002147 2147 GSM918410 Hardison Caltech-m 11907 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechHistC2c12Ab2621FCntrl50bPcr1xPkRep1 None Peaks Immortal cells Associated with the gene body of actively transcribed genes Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 H3K79me3 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeq Caltech RNA-seq GSE37909 RNA-seq from ENCODE/Caltech Expression and Regulation Description Rationale for the Mouse ENCODE project Our knowledge of the function of genomic DNA sequences comes from three basic approaches. Genetics uses changes in behavior or structure of a cell or organism in response to changes in DNA sequence to infer function of the altered sequence. Biochemical approaches monitor states of histone modification, binding of specific transcription factors, accessibility to DNases and other epigenetic features along genomic DNA. In general, these are associated with gene activity, but the precise relationships remain to be established. The third approach is evolutionary, using comparisons among homologous DNA sequences to find segments that are evolving more slowly or more rapidly than expected given the local rate of neutral change. These are inferred to be under negative or positive selection, respectively, and we interpret these as DNA sequences needed for a preserved (negative selection) or adaptive (positive selection) function. The ENCODE project aims to discover all the DNA sequences associated with various epigenetic features, with the reasonable expectation that these will also be functional (best tested by genetic methods). However, it is not clear how to relate these results with those from evolutionary analyses. The mouse ENCODE project aims to make this connection explicitly and with a moderate breadth. Assays identical to those being used in the ENCODE project are performed in cell types in mouse that are similar or homologous to those studied in the human project. Thus we will be able to discover which epigenetic features are conserved between mouse and human, and we can examine the extent to which these overlap with the DNA sequences under negative selection. The contribution of DNA with a function preserved in mammals versus that with a function in only one species will be discovered. The results will have a significant impact on our understanding of the evolution of gene regulation. Reference transcriptome measurements with RNA-seq 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). RNA-seq is performed by reverse-transcribing an RNA sample into cDNA, followed by high-throughput DNA sequencing, which was done here on the Illumina HiSeq sequencer. The transcriptome measurements shown on these tracks were performed on polyA selected RNA from total cellular RNA. PolyA-selected RNA was fragmented by magnesium-catalyzed hydrolysis and then converted into cDNA by random priming and amplified. Paired-end 2x100 bp reads were obtained from each end of a cDNA fragment. Reads were aligned to the mm9 human reference genome using TopHat (Trapnell et al., 2009), a program specifically designed to align RNA-seq reads and discover splice junctions de novo. All sequence and alignments files are available on the downloads page. 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 (BAM file) view shows reads aligned to the genome. Alignments are colored by cell type. See the Bowtie Manual (Langmead et al., 2009) for information about the SAM Bowtie output (including other tags) and the SAM Format Specification for information on the SAM/BAM file format. Raw Signal 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. This is used to display all reads in this track. Signal (Unique Reads) Density graph (wiggle) of signal enrichment based on processed data. This is used to display uniquely mapped reads in this track. Additional views are available on the Downloads page. 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. A quantity of 75 µgs 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. A quantity of 100 ngs of mRNA was then processed according to the protocol in Mortazavi et al. (2008), and prepared for sequencing on the Illumina GAIIx or HiSeq platforms according to the protocol for the ChIP-Seq DNA genomic DNA kit (Illumina). Paired-end libraries were size-selected around 200 bp (fragment length). Libraries were sequenced with the Illumina HiSeq according to the manufacturer's recommendations. Paired-end reads of 100 bp length were obtained Data Processing and Analysis Reads were mapped to the reference mouse genome (version mm9 with or without the Y chromosome, depending on the sex of the cell line, and without the random chromosomes in all cases) using TopHat (version 1.3.1). TopHat was used with default settings with the exception of specifying an empirically determined mean inner-mate distance and supplying known ENSEMBL version 63 splice junctions. Credits Wold Group: Brian Williams, Georgi Marinov, Diane Trout, Lorian Schaeffer, Gordon Kwan, Katherine Fisher, Gilberto De Salvo, Ali Mortazavi, Henry Amrhein, Brandon King 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. PMID: 19261174; PMC: PMC2690996 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. PMID: 18516045 Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. PMID: 19289445; PMC: PMC2672628 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. 
wgEncodeCaltechRnaSeqViewSignal Signal RNA-seq from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200SigRep1 C2C12 Myob Sig immortalized C2C12 RnaSeq ENCODE Mar 2012 Freeze 2012-04-17 2012-01-31 2012-11-31 wgEncodeEM002732 2732 GSM929774 Hardison Caltech-m 10985 TH131 2x75 1 longPolyA F C3H wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200SigRep1 None Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury Sequencing analysis of RNA expression Hardison Wold - Califonia Institute of Technology TopHat v1.3.1 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Female Strain C3H, Very related to C57BL/6 Signal C2C12 Myoblast RNA-seq Signal (Unique Reads) from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200E2p60hSigRep1 C2C12 Myoc Sig immortalized C2C12 RnaSeq ENCODE Mar 2012 Freeze 2012-04-18 2012-02-01 2012-11-01 wgEncodeEM002733 2733 GSM929775 Hardison Caltech-m 10986 TH131 2x75 1 longPolyA F C3H wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200E2p60hSigRep1 EqS_2.0pct_60hr Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury Sequencing analysis of RNA expression Hardison Wold - Califonia Institute of Technology TopHat v1.3.1 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Myocyte 60 h RNA-seq Signal (Unique Reads) from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200SigRep1 10T1/2 Fibb Sig immortalized 10T1/2 RnaSeq ENCODE Mar 2012 Freeze 2012-04-18 2012-03-20 2012-12-20 wgEncodeEM002735 2735 GSM929773 Hardison Caltech-m 11154 TH131 2x75 1 longPolyA F C3H wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200SigRep1 None Signal Immortal cells Multipotential cell line that can be converted by 5-azacytidine into three mesodermal stem cell lineages. Sequencing analysis of RNA expression Hardison Wold - Califonia Institute of Technology TopHat v1.3.1 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Female Strain C3H, Very related to C57BL/6 Signal 10T1/2 Fibroblast RNA-seq Signal (Unique Reads) from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200E2p60hSigRep1 10T1/2 Fibc Sig immortalized 10T1/2 RnaSeq ENCODE Mar 2012 Freeze 2012-04-18 2012-03-19 2012-12-19 wgEncodeEM002734 2734 GSM929772 Hardison Caltech-m 11155 TH131 2x75 1 longPolyA F C3H wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200E2p60hSigRep1 EqS_2.0pct_60hr Signal Immortal cells Multipotential cell line that can be converted by 5-azacytidine into three mesodermal stem cell lineages. Sequencing analysis of RNA expression Hardison Wold - Califonia Institute of Technology TopHat v1.3.1 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal 10T1/2 Fibrocyte 60 h RNA-seq Signal (Unique Reads) from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeqViewRawSignal RawSignal RNA-seq from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200RawRep1 C2C12 Myob Raw immortalized C2C12 RnaSeq ENCODE Mar 2012 Freeze 2012-04-18 2012-04-16 2013-01-16 wgEncodeEM002732 2732 GSM929774 Hardison Caltech-m 10985 TH131 2x75 1 longPolyA F C3H wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200RawRep1 None RawSignal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury Sequencing analysis of RNA expression Hardison Wold - Califonia Institute of Technology TopHat v1.3.1 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Female Strain C3H, Very related to C57BL/6 Shows the density of mapped reads on the plus and minus strands (wiggle format) C2C12 Myoblast RNA-seq Raw Signal from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200E2p60hRawRep1 C2C12 Myoc Raw immortalized C2C12 RnaSeq ENCODE Mar 2012 Freeze 2012-04-18 2012-04-16 2013-01-16 wgEncodeEM002733 2733 GSM929775 Hardison Caltech-m 10986 TH131 2x75 1 longPolyA F C3H wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200E2p60hRawRep1 EqS_2.0pct_60hr RawSignal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury Sequencing analysis of RNA expression Hardison Wold - Califonia Institute of Technology TopHat v1.3.1 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Shows the density of mapped reads on the plus and minus strands (wiggle format) C2C12 Myocyte 60 h RNA-seq Raw Signal from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200RawRep1 10T1/2 Fibb Raw immortalized 10T1/2 RnaSeq ENCODE Mar 2012 Freeze 2012-04-18 2012-04-16 2013-01-16 wgEncodeEM002735 2735 GSM929773 Hardison Caltech-m 11154 TH131 2x75 1 longPolyA F C3H wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200RawRep1 None RawSignal Immortal cells Multipotential cell line that can be converted by 5-azacytidine into three mesodermal stem cell lineages. Sequencing analysis of RNA expression Hardison Wold - Califonia Institute of Technology TopHat v1.3.1 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Female Strain C3H, Very related to C57BL/6 Shows the density of mapped reads on the plus and minus strands (wiggle format) 10T1/2 Fibroblast RNA-seq Raw Signal from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200E2p60hRawRep1 10T1/2 Fibc Raw immortalized 10T1/2 RnaSeq ENCODE Mar 2012 Freeze 2012-04-18 2012-04-16 2013-01-16 wgEncodeEM002734 2734 GSM929772 Hardison Caltech-m 11155 TH131 2x75 1 longPolyA F C3H wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200E2p60hRawRep1 EqS_2.0pct_60hr RawSignal Immortal cells Multipotential cell line that can be converted by 5-azacytidine into three mesodermal stem cell lineages. Sequencing analysis of RNA expression Hardison Wold - Califonia Institute of Technology TopHat v1.3.1 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Shows the density of mapped reads on the plus and minus strands (wiggle format) 10T1/2 Fibrocyte 60 h RNA-seq Raw Signal from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeqViewAlignments Alignments RNA-seq from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200AlnRep1 C2C12 Myob Aln immortalized C2C12 RnaSeq ENCODE Mar 2012 Freeze 2012-04-17 2012-01-31 2012-10-31 wgEncodeEM002732 2732 Hardison Caltech-m 10985 TH131 2x75 1 longPolyA F C3H wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200AlnRep1 None Alignments Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury Sequencing analysis of RNA expression Hardison Wold - Califonia Institute of Technology TopHat v1.3.1 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Female Strain C3H, Very related to C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch C2C12 Myoblast RNA-seq Alignments from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200E2p60hAlnRep1 C2C12 Myoc Aln immortalized C2C12 RnaSeq ENCODE Mar 2012 Freeze 2012-04-17 2012-01-31 2012-10-31 wgEncodeEM002733 2733 Hardison Caltech-m 10986 TH131 2x75 1 longPolyA F C3H wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200E2p60hAlnRep1 EqS_2.0pct_60hr Alignments Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury Sequencing analysis of RNA expression Hardison Wold - Califonia Institute of Technology TopHat v1.3.1 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Shows individual reads mapped to the genome and indicates where bases may mismatch C2C12 Myocyte 60 h RNA-seq Alignments from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200AlnRep1 10T1/2 Fibb Aln immortalized 10T1/2 RnaSeq ENCODE Mar 2012 Freeze 2012-04-18 2012-03-20 2012-12-20 wgEncodeEM002735 2735 Hardison Caltech-m 11154 TH131 2x75 1 longPolyA F C3H wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200AlnRep1 None Alignments Immortal cells Multipotential cell line that can be converted by 5-azacytidine into three mesodermal stem cell lineages. Sequencing analysis of RNA expression Hardison Wold - Califonia Institute of Technology TopHat v1.3.1 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Female Strain C3H, Very related to C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch 10T1/2 Fibroblast RNA-seq Alignments from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200E2p60hAlnRep1 10T1/2 Fibc Aln immortalized 10T1/2 RnaSeq ENCODE Mar 2012 Freeze 2012-04-18 2012-03-19 2012-12-19 wgEncodeEM002734 2734 Hardison Caltech-m 11155 TH131 2x75 1 longPolyA F C3H wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200E2p60hAlnRep1 EqS_2.0pct_60hr Alignments Immortal cells Multipotential cell line that can be converted by 5-azacytidine into three mesodermal stem cell lineages. Sequencing analysis of RNA expression Hardison Wold - Califonia Institute of Technology TopHat v1.3.1 Paired 75 nt reads Poly(A)+ RNA longer than 200 nt Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Shows individual reads mapped to the genome and indicates where bases may mismatch 10T1/2 Fibrocyte 60 h RNA-seq Alignments from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbs Caltech TFBS GSE36024 Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech Expression and Regulation Description Rationale for the Mouse ENCODE project Our knowledge of the function of genomic DNA sequences comes from three basic approaches. Genetics uses changes in behavior or structure of a cell or organism in response to changes in DNA sequence to infer function of the altered sequence. Biochemical approaches monitor states of histone modification, binding of specific transcription factors, accessibility to DNases and other epigenetic features along genomic DNA. In general, these are associated with gene activity, but the precise relationships remain to be established. The third approach is evolutionary, using comparisons among homologous DNA sequences to find segments that are evolving more slowly or more rapidly than expected given the local rate of neutral change. These are inferred to be under negative or positive selection, respectively, and we interpret these as DNA sequences needed for a preserved (negative selection) or adaptive (positive selection) function. The ENCODE project aims to discover all the DNA sequences associated with various epigenetic features, with the reasonable expectation that these will also be functional (best tested by genetic methods). However, it is not clear how to relate these results with those from evolutionary analyses. The mouse ENCODE project aims to make this connection explicitly and with a moderate breadth. Assays identical to those being used in the ENCODE project are performed in cell types in mouse that are similar or homologous to those studied in the human project. Thus, we will be able to discover which epigenetic features are conserved between mouse and human, and we can examine the extent to which these overlap with the DNA sequences under negative selection. The contribution of DNA that with a function preserved in mammals versus that with a function in only one species will be discovered. The results will have a significant impact on our understanding of the evolution of gene regulation. Maps of Occupancy by Transcription Factors Genome-wide occupancy maps of transcription factors (TFs) are generated by ChIP-seq. A ChIP-Seq experiment combines a chromatin immunoprecipitation (ChIP) experiment that enriches genomic DNA for the segments bound by specific proteins (the antigens recognized by the antibody) with high-throughput short read sequencing of the enriched DNA fragments (Wold & Myers, 2008). Proteins are crosslinked to DNA (usually with formaldehyde), chromatin is sheared and immunoprecipitated with the antibody of interest. The immunoprecipitated material is turned into a sequencing library and sequenced. The sequencing reads are then aligned to the genome. A control sample consisting of sonicated chromatin that has not been immunoprecipitated or immunoprecipitated with a non-specific immunoglobulin is also sequenced. The ChIP and the control datasets are analyzed with a variety of software packages to identify regions occupied by the target protein. The sequencing data, alignments and analysis files for 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. This track contains the following views: Peaks Regions of signal enrichment based on processed data. Intensity is represented in grayscale, the darker shading shows higher intensity (a solid vertical line in the peak region represents the point with the highest signal). Signal Density graph (wiggle) of signal enrichment based on processed data of all mapped read intensity of the signal is represented as RPM (Read 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. Chromatin immunoprecipitation followed published methods (Johnson & Mortazavi et al., 2007) with the exception of certain experiments for which glutaraldehyde was added to the crosslink reaction. Information on the antibodies used is available via the metadata for each subtrack. Libraries were constructed using the Illumina ChIP-seq Sample Preparation Kit or using a modified protocol that includes the addition of multiplexing tags to the fragments. DNA fragments were repaired to generate blunt ends and a single A nucleotide was added to each end. Double-stranded Illumina adaptors or Double-stranded Illumina adaptors with multiplexing tags were ligated to the fragments. Ligation products were amplified by 18 cycles of PCR, and the DNA between 150-250 bp was gel purified. Completed libraries were quantified with Quant-iT dsDNA HS Assay Kit. The DNA library was sequenced on the Illumina GAII and GAIIx sequencing systems, and more recently, for multiplexed libraries, several of them were pooled and sequenced on the HiSeq platform. Cluster generation, linearization, blocking and sequencing primer reagents were provided in the Illumina Cluster Amplification kits. Older libraries were generated using 2 rounds of PCR. Matched input samples were sequenced for each variation of fixation conditions and the number of PCR rounds. Reads of 32 bp, 36 bp or 50 bp length were generated. Sequencing reads (fastq files) were assigned to the corresponding libraries based on the multiplexing tag for pooled libraries (all tags have been removed from reads in the fastq files available for download) or directly processed. Bowtie (Langmead et al., 2009) was used to map reads to the male or female version of the mouse genome (excluding the _random chromosomes in the assembly) depending on the cell line sex. The following parameters were used: "-v 2 -k 11 -m 10 -t --best --strata". Aligned reads were converted into rds files using the ERANGE package (Johnson & Mortazavi et al., 2007) and the findall.py program in ERANGE was used to identify enriched regions against the matching input sample. The following settings were used for point-source transcription factors: "--shift learn --ratio 3 --minimum 2 --listPeak --revbackground". For histone modifications, the settings were changed to "--notrim --nodirectionality --spacing 100 --ratio 3 --minimum 2 --listPeak --revbackground". Credits Cell growth, ChIP, and Illumina library construction were done in the laboratory of Barbara Wold, (California Institute of Technology). Sequencing was done at the Millard and Muriel Jacobs Genetics and Genomics Laboratory at the California Institute of Technology, initial HiSeq data was generated at Illumina Inc., Hawyard, CA. Cell growth and ChIP: Georgi Marinov, Katherine Fisher, Gordon Kwan, Antony Kirilusha, Ali Mortazavi, Gilberto DeSalvo, Brian Williams Library Construction, Sequencing and Primary Data Handling: Lorianne Schaeffer, Diane Trout , Igor Antoschechkin (California Institute of Technology), Lu Zhang, Gary Schroth (Illumina Inc.) Data Processing and Submission: Georgi Marinov, Diane Trout Contact: Barbara Wold, Georgi K. Marinov, Diane Trout 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. 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. Wold B, Myers RM. Sequence census methods for functional genomics. Nat Methods. 2008 Jan;5(1):19-21. 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. 
wgEncodeCaltechTfbsViewSignal Signal Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Usf1FCntrl50bPcr1xSigRep1 C2 USF-1 1 immortalized USF-1 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002135 2135 GSM915162 Hardison Caltech-m 11923 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12Usf1FCntrl50bPcr1xSigRep1 None Signal Immortal cells 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. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 USF-1 Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Usf1FCntrl50bE2p60hPcr1xSigRep1 C2 USF-1 60h 1 immortalized USF-1 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002134 2134 GSM915161 Hardison Caltech-m 11644 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12Usf1FCntrl50bE2p60hPcr1xSigRep1 EqS_2.0pct_60hr Signal Immortal cells 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. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 USF-1 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Tcf3FCntrl32bE2p5dPcr2xSigRep1 C2 TCF3 5d 1 immortalized TCF3_(SC-349) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002121 2121 GSM915177 Hardison Caltech-m 10409 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Tcf3FCntrl32bE2p5dPcr2xSigRep1 EqS_2.0pct_5d Signal Immortal cells 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. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 5 d with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 TCF3 Myocyte 5d TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Tcf12FCntrl50bE2p60hPcr1xSigRep1 C2 TCF12 60h 1 immortalized TCF12 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002120 2120 GSM915178 Hardison Caltech-m 11719 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12Tcf12FCntrl50bE2p60hPcr1xSigRep1 EqS_2.0pct_60hr Signal Immortal cells 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. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 TCF12 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12SrfFCntrl32bE2p24hPcr2xSigRep1 C2 SRF 24h 1 immortalized SRF C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002119 2119 GSM915168 Hardison Caltech-m 10335 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12SrfFCntrl32bE2p24hPcr2xSigRep1 EqS_2.0pct_24hr Signal Immortal cells Serum response transcription factor Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 24 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 SRF Myocyte 24h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc32758FCntrl50bE2p7dPcr1xSigRep1 C2 MyoD 7d 1 immortalized MyoD_(sc-32758) C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002130 2130 GSM915165 Hardison Caltech-m 11926 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc32758FCntrl50bE2p7dPcr1xSigRep1 EqS_2.0pct_7d Signal Immortal cells This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 7 d with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 MyoD Myocyte 7d TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bPcr2xSigRep1 C2 MyoD 1 immortalized MyoD_(sc-32758) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002128 2128 GSM915186 Hardison Caltech-m 10333 Myoblast PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bPcr2xSigRep1 None Signal Immortal cells This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 MyoD Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p60hPcr2xSigRep1 C2 MyoD 60h 1 immortalized MyoD_(sc-32758) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002129 2129 GSM915185 Hardison Caltech-m 10481 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p60hPcr2xSigRep1 EqS_2.0pct_60hr Signal Immortal cells This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 MyoD Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p24hPcr2xSigRep1 C2 MyoD 24h 1 immortalized MyoD_(sc-32758) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002127 2127 GSM915183 Hardison Caltech-m 10296 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p24hPcr2xSigRep1 EqS_2.0pct_24hr Signal Immortal cells This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 24 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 MyoD Myocyte 24h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc12732FCntrl50bE2p7dPcr1xSigRep1 C2 Myogenin 7d 1 immortalized Myogenin_(sc-12732) C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002133 2133 GSM915164 Hardison Caltech-m 11927 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc12732FCntrl50bE2p7dPcr1xSigRep1 EqS_2.0pct_7d Signal Immortal cells Myogenin is a muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture. It is a member of a large family of proteins related by sequence homology, the helix-loop-helix (HLH) proteins. It is essential for the development of functional skeletal muscle. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 7 d with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Myogenin Myocyte 7d TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bPcr2xSigRep1 C2 Myogenin 1 immortalized Myogenin_(sc-12732) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002131 2131 GSM915166 Hardison Caltech-m 10599 Myoblast PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bPcr2xSigRep1 None Signal Immortal cells Myogenin is a muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture. It is a member of a large family of proteins related by sequence homology, the helix-loop-helix (HLH) proteins. It is essential for the development of functional skeletal muscle. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 Myogenin Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p60hPcr2xSigRep1 C2 Myogenin 60h 1 immortalized Myogenin_(sc-12732) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002132 2132 GSM915163 Hardison Caltech-m 10158 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p60hPcr2xSigRep1 EqS_2.0pct_60hr Signal Immortal cells Myogenin is a muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture. It is a member of a large family of proteins related by sequence homology, the helix-loop-helix (HLH) proteins. It is essential for the development of functional skeletal muscle. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Myogenin Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p24hPcr2xSigRep1 C2 Myogenin 24h 1 immortalized Myogenin_(sc-12732) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-09-01 2012-06-01 wgEncodeEM002136 2136 GSM915159 Hardison Caltech-m 10150 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p24hPcr2xSigRep1 EqS_2.0pct_24hr Signal Immortal cells Myogenin is a muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture. It is a member of a large family of proteins related by sequence homology, the helix-loop-helix (HLH) proteins. It is essential for the development of functional skeletal muscle. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 24 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Myogenin Myocyte 24h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Pol2s2FCntrl32bE2p60hPcr2xSigRep1 C2 Pol2S2 60h 1 immortalized Pol2(phosphoS2) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002118 2118 GSM915167 Hardison Caltech-m 10703 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Pol2s2FCntrl32bE2p60hPcr2xSigRep1 EqS_2.0pct_60hr Signal Immortal cells RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Pol2S2 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Pol2FCntrl32bE2p60hPcr2xSigRep1 C2 Pol2 60h 1 immortalized Pol2 C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002117 2117 GSM915176 Hardison Caltech-m 10704 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Pol2FCntrl32bE2p60hPcr2xSigRep1 EqS_2.0pct_60hr Signal Immortal cells RNA Polymerase II Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Pol2 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12NrsfFCntrl32bE2p60hPcr2xSigRep1 C2 NRSF 60h 1 immortalized NRSF C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002116 2116 GSM915175 Hardison Caltech-m 10065 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12NrsfFCntrl32bE2p60hPcr2xSigRep1 EqS_2.0pct_60hr Signal Immortal cells Neuron-restrictive silencer transcription factor Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 NRSF Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12MaxFCntrl50bPcr1xSigRep1 C2 Max 1 immortalized Max C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002115 2115 GSM915174 Hardison Caltech-m 11924 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12MaxFCntrl50bPcr1xSigRep1 None Signal Immortal cells 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). Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 Max Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12MaxFCntrl50bE2p60hPcr1xSigRep1 C2 Max 60h 1 immortalized Max C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002114 2114 GSM915173 Hardison Caltech-m 11682 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12MaxFCntrl50bE2p60hPcr1xSigRep1 EqS_2.0pct_60hr Signal Immortal cells 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). Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Max Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12InputFCntrl50bPcr1xSigRep1 C2 Con 50bp 1 immortalized Input C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002113 2113 GSM915172 Hardison Caltech-m 11612 Myoblast PCR1x 1 input F C3H wgEncodeCaltechTfbsC2c12InputFCntrl50bPcr1xSigRep1 None Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 Control 50bp Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12InputFCntrl50bE2p60hPcr1xSigRep2 C2 Con 50bp 60h 2 immortalized Input C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002126 2126 GSM915184 Hardison Caltech-m 11637 Myocyte PCR1x 2 input F C3H wgEncodeCaltechTfbsC2c12InputFCntrl50bE2p60hPcr1xSigRep2 EqS_2.0pct_60hr Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Control 50bp Myocyte 60h TFBS ChIP-seq Signal Rep 2 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12InputFCntrl50bE2p60hPcr1xSigRep1 C2 Con 50bp 60h 1 immortalized Input C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002126 2126 GSM915184 Hardison Caltech-m 11610 Myocyte PCR1x 1 input F C3H wgEncodeCaltechTfbsC2c12InputFCntrl50bE2p60hPcr1xSigRep1 EqS_2.0pct_60hr Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Control 50bp Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12InputFCntrl36bPcr1xSigRep1 C2 Con 36bp 1 immortalized Input C2C12 Control_36bp ChipSeq ENCODE Mar 2012 Freeze 2011-10-18 2012-07-18 wgEncodeEM002137 2137 GSM915160 Hardison Caltech-m 11612 PCR1x 1 input F C3H wgEncodeCaltechTfbsC2c12InputFCntrl36bPcr1xSigRep1 None Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 36 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 Control 36bp ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12InputFCntrl32bPcr2xSigRep1 C2 Con 32bp  1 immortalized Input C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002111 2111 GSM915170 Hardison Caltech-m 10135 Myoblast PCR2x 1 input F C3H wgEncodeCaltechTfbsC2c12InputFCntrl32bPcr2xSigRep1 None Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 Control 32bp Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12InputFCntrl32bE2p60hPcr2xSigRep1 C2 Con 32bp 60h 1 immortalized Input C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002112 2112 GSM915171 Hardison Caltech-m 10194 Myocyte PCR2x 1 input F C3H wgEncodeCaltechTfbsC2c12InputFCntrl32bE2p60hPcr2xSigRep1 EqS_2.0pct_60hr Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Control 32bp Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12InputFCntrl32bE2p24hPcr2xSigRep1 C2 Con 32bp 24h 1 immortalized Input C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002110 2110 GSM915169 Hardison Caltech-m 10007 Myocyte PCR2x 1 input F C3H wgEncodeCaltechTfbsC2c12InputFCntrl32bE2p24hPcr2xSigRep1 EqS_2.0pct_24hr Signal Immortal cells Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 24 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 Control 32bp Myocyte 24h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Fosl1sc605FCntrl36bPcr1xSigRep1 C2 FOSL1 1 immortalized FOSL1_(sc-605) C2C12 Control_36bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002124 2124 GSM915182 Hardison Caltech-m 11565 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12Fosl1sc605FCntrl36bPcr1xSigRep1 None Signal Immortal cells 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) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 36 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 FOSL1 Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12E2f4FCntrl50bE2p60hPcr1xSigRep1 C2 E2F4 60h 1 immortalized E2F4 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002109 2109 GSM915187 Hardison Caltech-m 11718 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12E2f4FCntrl50bE2p60hPcr1xSigRep1 EqS_2.0pct_60hr Signal Immortal cells mapping at the C-terminus of E2F4 of human origin Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 E2F4 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12CtcfFCntrl32bPcr2xSigRep1 C2 CTCF 1 immortalized CTCF C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002108 2108 GSM915188 Hardison Caltech-m 10506 Myoblast PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12CtcfFCntrl32bPcr2xSigRep1 None Signal Immortal cells CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 CTCF Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12CebpbFCntrl50bPcr1xSigRep1 C2 CEBPB 1 immortalized CEBPB C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002123 2123 GSM915179 Hardison Caltech-m 11942 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12CebpbFCntrl50bPcr1xSigRep1 None Signal Immortal cells Epitope mapping at the C-terminus of C/EBP-beta of rat origin Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Signal C2C12 CEBPB Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xSigRep2 C2 CEBPB 60h 2 immortalized CEBPB C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002122 2122 GSM915180 Hardison Caltech-m 11847 Myocyte PCR1x 2 exp F C3H wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xSigRep2 EqS_2.0pct_60hr Signal Immortal cells Epitope mapping at the C-terminus of C/EBP-beta of rat origin Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 CEBPB Myocyte 60h TFBS ChIP-seq Signal Rep 2 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xSigRep1 C2 CEBPB 60h 1 immortalized CEBPB C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002122 2122 GSM915180 Hardison Caltech-m 11653 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xSigRep1 EqS_2.0pct_60hr Signal Immortal cells Epitope mapping at the C-terminus of C/EBP-beta of rat origin Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Signal C2C12 CEBPB Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsViewPeaks Peaks Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Usf1FCntrl50bPcr1xPkRep1 C2 USF-1 1 immortalized USF-1 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002135 2135 GSM915162 Hardison Caltech-m 11923 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12Usf1FCntrl50bPcr1xPkRep1 None Peaks Immortal cells 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. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 USF-1 Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Usf1FCntrl50bE2p60hPcr1xPkRep1 C2 USF-1 60h 1 immortalized USF-1 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002134 2134 GSM915161 Hardison Caltech-m 11644 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12Usf1FCntrl50bE2p60hPcr1xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells 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. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 USF-1 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Tcf3FCntrl32bE2p5dPcr2xPkRep1 C2 TCF3 5d 1 immortalized TCF3_(SC-349) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002121 2121 GSM915177 Hardison Caltech-m 10409 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Tcf3FCntrl32bE2p5dPcr2xPkRep1 EqS_2.0pct_5d Peaks Immortal cells 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. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 5 d with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 TCF3 Myocyte 5d TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Tcf12FCntrl50bE2p60hPcr1xPkRep1 C2 TCF12 60h 1 immortalized TCF12 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002120 2120 GSM915178 Hardison Caltech-m 11719 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12Tcf12FCntrl50bE2p60hPcr1xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells 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. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 TCF12 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12SrfFCntrl32bE2p24hPcr2xPkRep1 C2 SRF 24h 1 immortalized SRF C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002119 2119 GSM915168 Hardison Caltech-m 10335 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12SrfFCntrl32bE2p24hPcr2xPkRep1 EqS_2.0pct_24hr Peaks Immortal cells Serum response transcription factor Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 24 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 SRF Myocyte 24h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc32758FCntrl50bE2p7dPcr1xPkRep1 C2 MyoD 7d 1 immortalized MyoD_(sc-32758) C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002130 2130 GSM915165 Hardison Caltech-m 11926 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc32758FCntrl50bE2p7dPcr1xPkRep1 EqS_2.0pct_7d Peaks Immortal cells This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 7 d with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 MyoD Myocyte 7d TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bPcr2xPkRep1 C2 MyoD 24h 1 immortalized MyoD_(sc-32758) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002128 2128 GSM915186 Hardison Caltech-m 10333 Myoblast PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bPcr2xPkRep1 None Peaks Immortal cells This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 MyoD Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p60hPcr2xPkRep1 C2 MyoD 60h 1 immortalized MyoD_(sc-32758) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002129 2129 GSM915185 Hardison Caltech-m 10481 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p60hPcr2xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 MyoD Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p24hPcr2xPkRep1 C2 MyoD 24h 1 immortalized MyoD_(sc-32758) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002127 2127 GSM915183 Hardison Caltech-m 10296 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p24hPcr2xPkRep1 EqS_2.0pct_24hr Peaks Immortal cells This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 24 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 MyoD Myocyte 24h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc12732FCntrl50bE2p7dPcr1xPkRep1 C2 Myogenin 7d 1 immortalized Myogenin_(sc-12732) C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002133 2133 GSM915164 Hardison Caltech-m 11927 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc12732FCntrl50bE2p7dPcr1xPkRep1 EqS_2.0pct_7d Peaks Immortal cells Myogenin is a muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture. It is a member of a large family of proteins related by sequence homology, the helix-loop-helix (HLH) proteins. It is essential for the development of functional skeletal muscle. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 7 d with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 Myogenin Myocyte 7d TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bPcr2xPkRep1 C2 Myogenin 1 immortalized Myogenin_(sc-12732) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002131 2131 GSM915166 Hardison Caltech-m 10599 Myoblast PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bPcr2xPkRep1 None Peaks Immortal cells Myogenin is a muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture. It is a member of a large family of proteins related by sequence homology, the helix-loop-helix (HLH) proteins. It is essential for the development of functional skeletal muscle. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 Myogenin Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p60hPcr2xPkRep1 C2 Myogenin 60h 1 immortalized Myogenin_(sc-12732) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002132 2132 GSM915163 Hardison Caltech-m 10158 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p60hPcr2xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells Myogenin is a muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture. It is a member of a large family of proteins related by sequence homology, the helix-loop-helix (HLH) proteins. It is essential for the development of functional skeletal muscle. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 Myogenin Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p24hPcr2xPkRep1 C2 Myogenin 24h 1 immortalized Myogenin_(sc-12732) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-09-01 2012-06-01 wgEncodeEM002136 2136 GSM915159 Hardison Caltech-m 10150 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p24hPcr2xPkRep1 EqS_2.0pct_24hr Peaks Immortal cells Myogenin is a muscle-specific transcription factor that can induce myogenesis in a variety of cell types in tissue culture. It is a member of a large family of proteins related by sequence homology, the helix-loop-helix (HLH) proteins. It is essential for the development of functional skeletal muscle. (provided by RefSeq) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 24 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 Myogenin Myocyte 24h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Pol2s2FCntrl32bE2p60hPcr2xPkRep1 C2 Pol2S2 60h 1 immortalized Pol2(phosphoS2) C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002118 2118 GSM915167 Hardison Caltech-m 10703 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Pol2s2FCntrl32bE2p60hPcr2xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 Pol2S2 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Pol2FCntrl32bE2p60hPcr2xPkRep1 C2 Pol2 60h 1 immortalized Pol2 C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002117 2117 GSM915176 Hardison Caltech-m 10704 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12Pol2FCntrl32bE2p60hPcr2xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells RNA Polymerase II Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 Pol2 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12NrsfFCntrl32bE2p60hPcr2xPkRep1 C2 NRSF 60h 1 immortalized NRSF C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002116 2116 GSM915175 Hardison Caltech-m 10065 Myocyte PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12NrsfFCntrl32bE2p60hPcr2xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells Neuron-restrictive silencer transcription factor Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 NRSF Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12MaxFCntrl50bPcr1xPkRep1 C2 Max Pk 1 immortalized Max C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002115 2115 GSM915174 Hardison Caltech-m 11924 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12MaxFCntrl50bPcr1xPkRep1 None Peaks Immortal cells 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). Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 Max Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12MaxFCntrl50bE2p60hPcr1xPkRep1 C2 Max 60h 1 immortalized Max C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002114 2114 GSM915173 Hardison Caltech-m 11682 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12MaxFCntrl50bE2p60hPcr1xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells 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). Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 Max Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12Fosl1sc605FCntrl36bPcr1xPkRep1 C2 FOSL1 1 immortalized FOSL1_(sc-605) C2C12 Control_36bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002124 2124 GSM915182 Hardison Caltech-m 11565 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12Fosl1sc605FCntrl36bPcr1xPkRep1 None Peaks Immortal cells 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) Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 36 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 FOSL1 Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12E2f4FCntrl50bE2p60hPcr1xPkRep1 C2 E2F4 60h 1 immortalized E2F4 C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002109 2109 GSM915187 Hardison Caltech-m 11718 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12E2f4FCntrl50bE2p60hPcr1xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells mapping at the C-terminus of E2F4 of human origin Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 E2F4 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12CtcfFCntrl32bPcr2xPkRep1 C2 CTCF 1 immortalized CTCF C2C12 Control_32bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-05 2012-05-05 wgEncodeEM002108 2108 GSM915188 Hardison Caltech-m 10506 Myoblast PCR2x 1 exp F C3H wgEncodeCaltechTfbsC2c12CtcfFCntrl32bPcr2xPkRep1 None Peaks Immortal cells CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 32 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 CTCF Myoblast ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12CebpbFCntrl50bPcr1xPkRep1 C2 CEBPB 1 immortalized CEBPB C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002123 2123 GSM915179 Hardison Caltech-m 11942 Myoblast PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12CebpbFCntrl50bPcr1xPkRep1 None Peaks Immortal cells Epitope mapping at the C-terminus of C/EBP-beta of rat origin Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 Regions of enriched signal in experiment C2C12 CEBPB Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xPkRep2 C2 CEBPB 60h 2 immortalized CEBPB C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002122 2122 GSM915180 Hardison Caltech-m 11847 Myocyte PCR1x 2 exp F C3H wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xPkRep2 EqS_2.0pct_60hr Peaks Immortal cells Epitope mapping at the C-terminus of C/EBP-beta of rat origin Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 CEBPB Myocyte 60h TFBS ChIP-seq Peaks Rep 2 from ENCODE/Caltech Expression and Regulation 
wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xPkRep1 C2 CEBPB 60h 1 immortalized CEBPB C2C12 Control_50bp ChipSeq ENCODE Mar 2012 Freeze 2011-08-11 2012-05-11 wgEncodeEM002122 2122 GSM915180 Hardison Caltech-m 11653 Myocyte PCR1x 1 exp F C3H wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xPkRep1 EqS_2.0pct_60hr Peaks Immortal cells Epitope mapping at the C-terminus of C/EBP-beta of rat origin Myoblast cell line derived from thigh muscle of C3H mice after crush injury This data represents a control being compared to experiments using read length of 50 bp Chromatin IP Sequencing Hardison Wold - Califonia Institute of Technology one 15-cycle round of PCR (Myers) Female Strain C3H, Very related to C57BL/6 60 h with 2.0% Equine Serum and Insulin (Wold) Regions of enriched signal in experiment C2C12 CEBPB Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech Expression and Regulation 
ccdsGene CCDS Consensus CDS Genes and Gene Predictions Description This track shows mouse genome high-confidence gene annotations from the Consensus Coding Sequence (CCDS) project. This project is a collaborative effort to identify a core set of mouse protein-coding regions that are consistently annotated and of high quality. The long-term goal is to support convergence towards a standard set of gene annotations on the mouse genome. Collaborators include: European Bioinformatics Institute (EBI) National Center for Biotechnology Information (NCBI) University of California, Santa Cruz (UCSC) Wellcome Trust Sanger Institute (WTSI) For more information on the different gene tracks, see our Genes FAQ. Methods CDS annotations of the mouse genome were obtained from two sources: NCBI RefSeq and a union of the gene annotations from Ensembl and Vega, collectively known as Hinxton. Genes with identical CDS genomic coordinates in both sets become CCDS candidates. The genes undergo a quality evaluation, which must be approved by all collaborators. The following criteria are currently used to assess each gene: an initiating ATG (Exception: a non-ATG translation start codon is annotated if it has sufficient experimental support), a valid stop codon, and no in-frame stop codons (Exception: selenoproteins, which contain a TGA codon that is known to be translated to a selenocysteine instead of functioning as a stop codon) ability to be translated from the genome reference sequence without frameshifts recognizable splicing sites no intersection with putative pseudogene predictions supporting transcripts and protein homology conservation evidence with other species A unique CCDS ID is assigned to the CCDS, which links together all gene annotations with the same CDS. CCDS gene annotations are under continuous review, with periodic updates to this track. Credits This track was produced at UCSC from data downloaded from the CCDS project web site. References Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41. PMID: 11752248; PMC: PMC99161 Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009 Jul;19(7):1316-23. PMID: 19498102; PMC: PMC2704439 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979 
cytoBand Chromosome Band Chromosome Bands Based On Microscopy Mapping and Sequencing Description The chromosome band track represents the approximate location of bands seen on Giemsa-stained chromosomes. Methods Data are derived from the ideogram.gz file downloaded from the NCBI ftp site ftp://ftp.ncbi.nlm.nih.gov/pub/gdp/ (NCBI current version only). Band lengths are typically estimated based on FISH or other molecular markers interpreted via microscopy. Credits We would like to thank NCBI for providing this information. Please direct any inquires into the exact method used for each organism to NCBI. 
cytoBandIdeo Chromosome Band (Ideogram) Chromosome Bands Based on Microscopy (for Ideogram) Mapping and Sequencing 
crisprRanges CRISPR Regions Genome regions processed to find CRISPR/Cas9 target sites (exons +/- 200 bp) Genes and Gene Predictions Description This track shows regions of the genome within 200 bp of transcribed regions and DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme from S. pyogenes (PAM: NGG). CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms through the tool CRISPOR. Display Conventions and Configuration The track &quot;CRISPR Regions&quot; shows the regions of the genome where target sites were analyzed, i.e. within 200 bp of transcribed regions as annotated by Ensembl transcript models. The track &quot;CRISPR Targets&quot; shows the target sites in these regions. The target sequence of the guide is shown with a thick (exon) bar. The PAM motif match (NGG) is shown with a thinner bar. Guides are colored to reflect both predicted specificity and efficiency. Specificity reflects the &quot;uniqueness&quot; of a 20mer sequence in the genome; the less unique a sequence is, the more likely it is to cleave other locations of the genome (off-target effects). Efficiency is the frequency of cleavage at the target site (on-target efficiency). Shades of gray stand for sites that are hard to target specifically, as the 20mer is not very unique in the genome: impossible to target: target site has at least one identical copy in the genome and was not scored hard to target: many similar sequences in the genome that alignment stopped, repeat? hard to target: target site was aligned but results in a low specificity score &lt;= 50 (see below) Colors highlight targets that are specific in the genome (MIT specificity &gt; 50) but have different predicted efficiencies: unable to calculate Doench/Fusi 2016 efficiency score low predicted cleavage: Doench/Fusi 2016 Efficiency percentile &lt;= 30 medium predicted cleavage: Doench/Fusi 2016 Efficiency percentile &gt; 30 and &lt; 55 high predicted cleavage: Doench/Fusi 2016 Efficiency &gt; 55 Mouse-over a target site to show predicted specificity and efficiency scores: The MIT Specificity score summarizes all off-targets into a single number from 0-100. The higher the number, the fewer off-target effects are expected. We recommend guides with an MIT specificity &gt; 50. The efficiency score tries to predict if a guide leads to rather strong or weak cleavage. According to (Haeussler et al. 2016), the Doench 2016 Efficiency score should be used to select the guide with the highest cleavage efficiency when expressing guides from RNA PolIII Promoters such as U6. Scores are given as percentiles, e.g. &quot;70%&quot; means that 70% of mammalian guides have a score equal or lower than this guide. The raw score number is also shown in parentheses after the percentile. The Moreno-Mateos 2015 Efficiency score should be used instead of the Doench 2016 score when transcribing the guide in vitro with a T7 promoter, e.g. for injections in mouse, zebrafish or Xenopus embryos. The Moreno-Mateos score is given in percentiles and the raw value in parentheses, see the note above. Click onto features to show all scores and predicted off-targets with up to four mismatches. The Out-of-Frame score by Bae et al. 2014 is correlated with the probability that mutations induced by the guide RNA will disrupt the open reading frame. The authors recommend out-of-frame scores &gt; 66 to create knock-outs with a single guide efficiently. Off-target sites are sorted by the CFD (Cutting Frequency Determination) score (Doench et al. 2016). The higher the CFD score, the more likely there is off-target cleavage at that site. Off-targets with a CFD score &lt; 0.023 are not shown on this page, but are availble when following the link to the external CRISPOR tool. When compared against experimentally validated off-targets by Haeussler et al. 2016, the large majority of predicted off-targets with CFD scores &lt; 0.023 were false-positives. Methods Relationship between predictions and experimental data Like most algorithms, the MIT specificity score is not always a perfect predictor of off-target effects. Despite low scores, many tested guides caused few and/or weak off-target cleavage when tested with whole-genome assays (Figure 2 from Haeussler et al. 2016), as shown below, and the published data contains few data points with high specificity scores. Overall though, the assays showed that the higher the specificity score, the lower the off-target effects. Similarly, efficiency scoring is not very accurate: guides with low scores can be efficient and vice versa. As a general rule, however, the higher the score, the less likely that a guide is very inefficient. The following histograms illustrate, for each type of score, how the share of inefficient guides drops with increasing efficiency scores: When reading this plot, keep in mind that both scores were evaluated on their own training data. Especially for the Moreno-Mateos score, the results are too optimistic, due to overfitting. When evaluated on independent datasets, the correlation of the prediction with other assays was around 25% lower, see Haeussler et al. 2016. At the time of writing, there is no independent dataset available yet to determine the Moreno-Mateos accuracy for each score percentile range. Track methods Exons as predicted by Ensembl Gene models were used, extended by 200 basepairs on each side, searched for the -NGG motif. Flanking 20mer guide sequences were aligned to the genome with BWA and scored with MIT Specificity scores using the command-line version of crispor.org. Non-unique guide sequences were skipped. Flanking sequences were extracted from the genome and input for Crispor efficiency scoring, available from the Crispor downloads page, which includes the Doench 2016, Moreno-Mateos 2015 and Bae 2014 algorithms, among others. Data Access The raw data can be explored interactively with the Table Browser. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The files for this track are called crispr.bb and crisprDetails.tab and are located in the /gbdb/mm9/crispr directory of our downloads server. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/crisprRanges/crispr.bb -chrom=chr21 -start=0 -end=10000000 stdout The file crisprDetails.tab includes the details of the off-targets. The last column of the bigBed file is the offset of the respective line in crisprDetails.tab. E.g. if the last column is 14227033723, then the following command will extract the line with the corresponding off-target details: curl -s -r 14227033723-14227043723 http://hgdownload.soe.ucsc.edu/gbdb/hg19/crispr/crisprDetails.tab | head -n1. The off-target details can currently not be joined with the table browser. The file crisprDetails.tab is a tab-separated text file with two fields. The first field contains the numbers of off-targets for each mismatch, e.g. "0,0,1,3,49" means 0 off-targets at zero mismatches, 1 at two mismatches, 3 at three and 49 off-targets at four mismatches. The second field is a pipe-separated list of semicolon-separated tuples with the genome coordinates and the CFD score. E.g. "chr10;123376795+;42|chr5;148353274-;39" describes two off-targets, with the first at chr1:123376795 on the positive strand and a CFD score 0.42 Credits Track created by Maximilian Haeussler and Hiram Clawson, with helpful input from Jean-Paul Concordet (MNHN Paris) and Alberto Stolfi (NYU). References Haeussler M, Sch&#246;nig K, Eckert H, Eschstruth A, Miann&#233; J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 2016 Jul 5;17(1):148. PMID: 27380939; PMC: PMC4934014 Bae S, Kweon J, Kim HS, Kim JS. Microhomology-based choice of Cas9 nuclease target sites. Nat Methods. 2014 Jul;11(7):705-6. PMID: 24972169 Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016 Feb;34(2):184-91. PMID: 26780180; PMC: PMC4744125 Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013 Sep;31(9):827-32. PMID: 23873081; PMC: PMC3969858 Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods. 2015 Oct;12(10):982-8. PMID: 26322839; PMC: PMC4589495 
crispr CRISPR CRISPR/Cas9 Sp. Pyog. target sites Genes and Gene Predictions Description This track shows regions of the genome within 200 bp of transcribed regions and DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme from S. pyogenes (PAM: NGG). CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms through the tool CRISPOR. Display Conventions and Configuration The track &quot;CRISPR Regions&quot; shows the regions of the genome where target sites were analyzed, i.e. within 200 bp of transcribed regions as annotated by Ensembl transcript models. The track &quot;CRISPR Targets&quot; shows the target sites in these regions. The target sequence of the guide is shown with a thick (exon) bar. The PAM motif match (NGG) is shown with a thinner bar. Guides are colored to reflect both predicted specificity and efficiency. Specificity reflects the &quot;uniqueness&quot; of a 20mer sequence in the genome; the less unique a sequence is, the more likely it is to cleave other locations of the genome (off-target effects). Efficiency is the frequency of cleavage at the target site (on-target efficiency). Shades of gray stand for sites that are hard to target specifically, as the 20mer is not very unique in the genome: impossible to target: target site has at least one identical copy in the genome and was not scored hard to target: many similar sequences in the genome that alignment stopped, repeat? hard to target: target site was aligned but results in a low specificity score &lt;= 50 (see below) Colors highlight targets that are specific in the genome (MIT specificity &gt; 50) but have different predicted efficiencies: unable to calculate Doench/Fusi 2016 efficiency score low predicted cleavage: Doench/Fusi 2016 Efficiency percentile &lt;= 30 medium predicted cleavage: Doench/Fusi 2016 Efficiency percentile &gt; 30 and &lt; 55 high predicted cleavage: Doench/Fusi 2016 Efficiency &gt; 55 Mouse-over a target site to show predicted specificity and efficiency scores: The MIT Specificity score summarizes all off-targets into a single number from 0-100. The higher the number, the fewer off-target effects are expected. We recommend guides with an MIT specificity &gt; 50. The efficiency score tries to predict if a guide leads to rather strong or weak cleavage. According to (Haeussler et al. 2016), the Doench 2016 Efficiency score should be used to select the guide with the highest cleavage efficiency when expressing guides from RNA PolIII Promoters such as U6. Scores are given as percentiles, e.g. &quot;70%&quot; means that 70% of mammalian guides have a score equal or lower than this guide. The raw score number is also shown in parentheses after the percentile. The Moreno-Mateos 2015 Efficiency score should be used instead of the Doench 2016 score when transcribing the guide in vitro with a T7 promoter, e.g. for injections in mouse, zebrafish or Xenopus embryos. The Moreno-Mateos score is given in percentiles and the raw value in parentheses, see the note above. Click onto features to show all scores and predicted off-targets with up to four mismatches. The Out-of-Frame score by Bae et al. 2014 is correlated with the probability that mutations induced by the guide RNA will disrupt the open reading frame. The authors recommend out-of-frame scores &gt; 66 to create knock-outs with a single guide efficiently. Off-target sites are sorted by the CFD (Cutting Frequency Determination) score (Doench et al. 2016). The higher the CFD score, the more likely there is off-target cleavage at that site. Off-targets with a CFD score &lt; 0.023 are not shown on this page, but are availble when following the link to the external CRISPOR tool. When compared against experimentally validated off-targets by Haeussler et al. 2016, the large majority of predicted off-targets with CFD scores &lt; 0.023 were false-positives. Methods Relationship between predictions and experimental data Like most algorithms, the MIT specificity score is not always a perfect predictor of off-target effects. Despite low scores, many tested guides caused few and/or weak off-target cleavage when tested with whole-genome assays (Figure 2 from Haeussler et al. 2016), as shown below, and the published data contains few data points with high specificity scores. Overall though, the assays showed that the higher the specificity score, the lower the off-target effects. Similarly, efficiency scoring is not very accurate: guides with low scores can be efficient and vice versa. As a general rule, however, the higher the score, the less likely that a guide is very inefficient. The following histograms illustrate, for each type of score, how the share of inefficient guides drops with increasing efficiency scores: When reading this plot, keep in mind that both scores were evaluated on their own training data. Especially for the Moreno-Mateos score, the results are too optimistic, due to overfitting. When evaluated on independent datasets, the correlation of the prediction with other assays was around 25% lower, see Haeussler et al. 2016. At the time of writing, there is no independent dataset available yet to determine the Moreno-Mateos accuracy for each score percentile range. Track methods Exons as predicted by Ensembl Gene models were used, extended by 200 basepairs on each side, searched for the -NGG motif. Flanking 20mer guide sequences were aligned to the genome with BWA and scored with MIT Specificity scores using the command-line version of crispor.org. Non-unique guide sequences were skipped. Flanking sequences were extracted from the genome and input for Crispor efficiency scoring, available from the Crispor downloads page, which includes the Doench 2016, Moreno-Mateos 2015 and Bae 2014 algorithms, among others. Data Access The raw data can be explored interactively with the Table Browser. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The files for this track are called crispr.bb and crisprDetails.tab and are located in the /gbdb/mm9/crispr directory of our downloads server. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/crispr/crispr.bb -chrom=chr21 -start=0 -end=10000000 stdout The file crisprDetails.tab includes the details of the off-targets. The last column of the bigBed file is the offset of the respective line in crisprDetails.tab. E.g. if the last column is 14227033723, then the following command will extract the line with the corresponding off-target details: curl -s -r 14227033723-14227043723 http://hgdownload.soe.ucsc.edu/gbdb/hg19/crispr/crisprDetails.tab | head -n1. The off-target details can currently not be joined with the table browser. The file crisprDetails.tab is a tab-separated text file with two fields. The first field contains the numbers of off-targets for each mismatch, e.g. "0,0,1,3,49" means 0 off-targets at zero mismatches, 1 at two mismatches, 3 at three and 49 off-targets at four mismatches. The second field is a pipe-separated list of semicolon-separated tuples with the genome coordinates and the CFD score. E.g. "chr10;123376795+;42|chr5;148353274-;39" describes two off-targets, with the first at chr1:123376795 on the positive strand and a CFD score 0.42 Credits Track created by Maximilian Haeussler and Hiram Clawson, with helpful input from Jean-Paul Concordet (MNHN Paris) and Alberto Stolfi (NYU). References Haeussler M, Sch&#246;nig K, Eckert H, Eschstruth A, Miann&#233; J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 2016 Jul 5;17(1):148. PMID: 27380939; PMC: PMC4934014 Bae S, Kweon J, Kim HS, Kim JS. Microhomology-based choice of Cas9 nuclease target sites. Nat Methods. 2014 Jul;11(7):705-6. PMID: 24972169 Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016 Feb;34(2):184-91. PMID: 26780180; PMC: PMC4744125 Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013 Sep;31(9):827-32. PMID: 23873081; PMC: PMC3969858 Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods. 2015 Oct;12(10):982-8. PMID: 26322839; PMC: PMC4589495 
crisprTargets CRISPR Targets CRISPR/Cas9 -NGG Targets Genes and Gene Predictions Description This track shows regions of the genome within 200 bp of transcribed regions and DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme from S. pyogenes (PAM: NGG). CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms through the tool CRISPOR. Display Conventions and Configuration The track &quot;CRISPR Regions&quot; shows the regions of the genome where target sites were analyzed, i.e. within 200 bp of transcribed regions as annotated by Ensembl transcript models. The track &quot;CRISPR Targets&quot; shows the target sites in these regions. The target sequence of the guide is shown with a thick (exon) bar. The PAM motif match (NGG) is shown with a thinner bar. Guides are colored to reflect both predicted specificity and efficiency. Specificity reflects the &quot;uniqueness&quot; of a 20mer sequence in the genome; the less unique a sequence is, the more likely it is to cleave other locations of the genome (off-target effects). Efficiency is the frequency of cleavage at the target site (on-target efficiency). Shades of gray stand for sites that are hard to target specifically, as the 20mer is not very unique in the genome: impossible to target: target site has at least one identical copy in the genome and was not scored hard to target: many similar sequences in the genome that alignment stopped, repeat? hard to target: target site was aligned but results in a low specificity score &lt;= 50 (see below) Colors highlight targets that are specific in the genome (MIT specificity &gt; 50) but have different predicted efficiencies: unable to calculate Doench/Fusi 2016 efficiency score low predicted cleavage: Doench/Fusi 2016 Efficiency percentile &lt;= 30 medium predicted cleavage: Doench/Fusi 2016 Efficiency percentile &gt; 30 and &lt; 55 high predicted cleavage: Doench/Fusi 2016 Efficiency &gt; 55 Mouse-over a target site to show predicted specificity and efficiency scores: The MIT Specificity score summarizes all off-targets into a single number from 0-100. The higher the number, the fewer off-target effects are expected. We recommend guides with an MIT specificity &gt; 50. The efficiency score tries to predict if a guide leads to rather strong or weak cleavage. According to (Haeussler et al. 2016), the Doench 2016 Efficiency score should be used to select the guide with the highest cleavage efficiency when expressing guides from RNA PolIII Promoters such as U6. Scores are given as percentiles, e.g. &quot;70%&quot; means that 70% of mammalian guides have a score equal or lower than this guide. The raw score number is also shown in parentheses after the percentile. The Moreno-Mateos 2015 Efficiency score should be used instead of the Doench 2016 score when transcribing the guide in vitro with a T7 promoter, e.g. for injections in mouse, zebrafish or Xenopus embryos. The Moreno-Mateos score is given in percentiles and the raw value in parentheses, see the note above. Click onto features to show all scores and predicted off-targets with up to four mismatches. The Out-of-Frame score by Bae et al. 2014 is correlated with the probability that mutations induced by the guide RNA will disrupt the open reading frame. The authors recommend out-of-frame scores &gt; 66 to create knock-outs with a single guide efficiently. Off-target sites are sorted by the CFD (Cutting Frequency Determination) score (Doench et al. 2016). The higher the CFD score, the more likely there is off-target cleavage at that site. Off-targets with a CFD score &lt; 0.023 are not shown on this page, but are availble when following the link to the external CRISPOR tool. When compared against experimentally validated off-targets by Haeussler et al. 2016, the large majority of predicted off-targets with CFD scores &lt; 0.023 were false-positives. Methods Relationship between predictions and experimental data Like most algorithms, the MIT specificity score is not always a perfect predictor of off-target effects. Despite low scores, many tested guides caused few and/or weak off-target cleavage when tested with whole-genome assays (Figure 2 from Haeussler et al. 2016), as shown below, and the published data contains few data points with high specificity scores. Overall though, the assays showed that the higher the specificity score, the lower the off-target effects. Similarly, efficiency scoring is not very accurate: guides with low scores can be efficient and vice versa. As a general rule, however, the higher the score, the less likely that a guide is very inefficient. The following histograms illustrate, for each type of score, how the share of inefficient guides drops with increasing efficiency scores: When reading this plot, keep in mind that both scores were evaluated on their own training data. Especially for the Moreno-Mateos score, the results are too optimistic, due to overfitting. When evaluated on independent datasets, the correlation of the prediction with other assays was around 25% lower, see Haeussler et al. 2016. At the time of writing, there is no independent dataset available yet to determine the Moreno-Mateos accuracy for each score percentile range. Track methods Exons as predicted by Ensembl Gene models were used, extended by 200 basepairs on each side, searched for the -NGG motif. Flanking 20mer guide sequences were aligned to the genome with BWA and scored with MIT Specificity scores using the command-line version of crispor.org. Non-unique guide sequences were skipped. Flanking sequences were extracted from the genome and input for Crispor efficiency scoring, available from the Crispor downloads page, which includes the Doench 2016, Moreno-Mateos 2015 and Bae 2014 algorithms, among others. Data Access The raw data can be explored interactively with the Table Browser. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The files for this track are called crispr.bb and crisprDetails.tab and are located in the /gbdb/mm9/crispr directory of our downloads server. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/crisprTargets/crispr.bb -chrom=chr21 -start=0 -end=10000000 stdout The file crisprDetails.tab includes the details of the off-targets. The last column of the bigBed file is the offset of the respective line in crisprDetails.tab. E.g. if the last column is 14227033723, then the following command will extract the line with the corresponding off-target details: curl -s -r 14227033723-14227043723 http://hgdownload.soe.ucsc.edu/gbdb/hg19/crispr/crisprDetails.tab | head -n1. The off-target details can currently not be joined with the table browser. The file crisprDetails.tab is a tab-separated text file with two fields. The first field contains the numbers of off-targets for each mismatch, e.g. "0,0,1,3,49" means 0 off-targets at zero mismatches, 1 at two mismatches, 3 at three and 49 off-targets at four mismatches. The second field is a pipe-separated list of semicolon-separated tuples with the genome coordinates and the CFD score. E.g. "chr10;123376795+;42|chr5;148353274-;39" describes two off-targets, with the first at chr1:123376795 on the positive strand and a CFD score 0.42 Credits Track created by Maximilian Haeussler and Hiram Clawson, with helpful input from Jean-Paul Concordet (MNHN Paris) and Alberto Stolfi (NYU). References Haeussler M, Sch&#246;nig K, Eckert H, Eschstruth A, Miann&#233; J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 2016 Jul 5;17(1):148. PMID: 27380939; PMC: PMC4934014 Bae S, Kweon J, Kim HS, Kim JS. Microhomology-based choice of Cas9 nuclease target sites. Nat Methods. 2014 Jul;11(7):705-6. PMID: 24972169 Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016 Feb;34(2):184-91. PMID: 26780180; PMC: PMC4744125 Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013 Sep;31(9):827-32. PMID: 23873081; PMC: PMC3969858 Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods. 2015 Oct;12(10):982-8. PMID: 26322839; PMC: PMC4589495 
wgEncodeCshlLongRnaSeq CSHL Long RNA-seq GSE36025 Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression and Regulation Description These tracks were generated by the ENCODE Consortium. They contain information about mouse RNAs greater than 200 nucleotides in length obtained as short reads off the Illumina platform. Data are available from 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. Raw Signals The Plus Raw Signal and Minus Raw 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 of Bowtie output. 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. 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 Tissue Samples Individual tissues were harvested from mouse strain C57BL/6J at different timepoints according to ENCODE cell culture protocols. Whenever possible, biological replicates were obtained from littermates. 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 spike-in sequence and the concentrations are available for download in the supplemental directory. Sequencing and Mapping The libraries were sequenced on the Illumina platform (either GAIIx or Hi-Seq) in mate-pair fashion (either pair-end 76 or pair-end 101) to an average depth of 100 million mate-pairs. The data were mapped against mm9 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&#37;. 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 exons and Spearman correlation coefficients were computed. In general, Rho values are greater than 0.90 between biological replicates. Release Notes This is release 3 (Sept 2012) of this track. It adds data for bladder, cerebellum, CNS, cortex, frontal lobe, limb, liver, placenta, and whole brain. The samples for CNS, liver, limb and whole brain vary over age (developmental stage). This release also contains replacement BAM files for the previous ones had the second read reverse complemented. Credits These data were generated and analyzed by the transcriptome group at Cold Spring Harbor Laboratories and the Center for Genomic Regulation (CRG in Barcelona), who are participants in the ENCODE Transcriptome Group. Contacts: Carrie Davis (experimental), Roderic Guigo and lab (data processing), Tom Gingeras (primary investigator) References 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. PMID: 21816910; PMC: PMC3166838 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. PMID: 19620212; PMC: PMC2764448 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 and Regulation 
wgEncodeCshlLongRnaSeqWbrainE14halfJunctions WholeBrain J E14.5 WholeBrain RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003055 3055 GSM1000572 Gingeras CSHL-m LID46987,LID46988 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqWbrainE14halfJunctions Junctions Embryonic day 14.5 Whole Brain 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Whole Brain E14.5 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqThymusAdult8wksJunctions Thymus J adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002518 2518 GSM900192 Gingeras CSHL-m LID20922,LID20923 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqThymusAdult8wksJunctions Junctions Adult 8 weeks Thymus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Thymus A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqTestisAdult8wksJunctions Testis J adult-8wks Testis RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002519 2519 GSM900193 Gingeras CSHL-m LID20868,LID20869 iIDR cell 2x76D longPolyA Illumina_GA2x M C57BL/6J wgEncodeCshlLongRnaSeqTestisAdult8wksJunctions Junctions Adult 8 weeks Testis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Male A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Testis A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSfatAdult8wksJunctions SubcFatPad J adult-8wks SubcFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002528 2528 GSM900191 Gingeras CSHL-m LID21181,LID21182 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSfatAdult8wksJunctions Junctions Adult 8 weeks Subcutaneous Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Subcutaneous Fat Pad A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqStomAdult8wksJunctions Stomach J adult-8wks Stomach RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002527 2527 GSM900185 Gingeras CSHL-m LID20732,LID20733 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqStomAdult8wksJunctions Junctions Adult 8 weeks Stomach Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Stomach A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSpleenAdult8wksJunctions Spleen J adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002517 2517 GSM900197 Gingeras CSHL-m LID21038,LID21039 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSpleenAdult8wksJunctions Junctions Adult 8 weeks Spleen Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Spleen A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSmintAdult8wksJunctions SmInt J adult-8wks SmIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002526 2526 GSM900186 Gingeras CSHL-m LID20819,LID20820 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSmintAdult8wksJunctions Junctions Adult 8 weeks Small Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Small Intestine A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqPlacAdult8wksJunctions Placenta J adult-8wks Placenta RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003061 3061 GSM1000565 Gingeras CSHL-m LID46983,LID46984 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqPlacAdult8wksJunctions Junctions Adult 8 weeks Placenta 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Placenta A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqOvaryAdult8wksJunctions Ovary J adult-8wks Ovary RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002525 2525 GSM900183 Gingeras CSHL-m LID20821,LID20822 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqOvaryAdult8wksJunctions Junctions Adult 8 weeks Ovary Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Ovary A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqMamgAdult8wksJunctions MaGland J adult-8wks MammaryGland RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002524 2524 GSM900184 Gingeras CSHL-m LID20924,LID20925 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqMamgAdult8wksJunctions Junctions Adult 8 weeks Mammary Gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Mammary Gland A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLungAdult8wksJunctions Lung J adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002516 2516 GSM900196 Gingeras CSHL-m LID20920,LID20921 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLungAdult8wksJunctions Junctions Adult 8 weeks Lung Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Lung A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE18Junctions Liver E18 J E18 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003060 3060 GSM1000566 Gingeras CSHL-m LID47148,LID47149 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE18Junctions Junctions Embryonic day 18 Liver 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Liver E18 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14halfJunctions Liver E14.5 J E14.5 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEM003054 3054 GSM1000571 Gingeras CSHL-m LID47146,LID47147 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14halfJunctions Junctions Embryonic day 14.5 Liver 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Liver E14.5 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14Junctions Liver E14 J E14 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003053 3053 GSM1000574 Gingeras CSHL-m LID47144,LID47145 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14Junctions Junctions Embryonic day 14 Liver 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Liver E14 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverAdult8wksJunctions Liver A8 J adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002515 2515 GSM900195 Gingeras CSHL-m LID21042,LID21043 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLiverAdult8wksJunctions Junctions Adult 8 weeks Liver Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Liver A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLimbE14halfJunctions Limb J E14.5 Limb RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003059 3059 GSM1000568 Gingeras CSHL-m LID46985,LID46986 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLimbE14halfJunctions Junctions Embryonic day 14.5 Limb 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Limb E14.5 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLgintAdult8wksJunctions LgInt J adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002523 2523 GSM900189 Gingeras CSHL-m LID21183,LID21184 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLgintAdult8wksJunctions Junctions Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Large Intestine A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqKidneyAdult8wksJunctions Kidney J adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002514 2514 GSM900194 Gingeras CSHL-m LID20872,LID20873 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqKidneyAdult8wksJunctions Junctions Adult 8 weeks Kidney Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Kidney A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqHeartAdult8wksJunctions Heart J adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002513 2513 GSM900199 Gingeras CSHL-m LID20871,LID20870 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqHeartAdult8wksJunctions Junctions Adult 8 weeks Heart Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Heart A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqGfatAdult8wksJunctions GenFatPad J adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002522 2522 GSM900190 Gingeras CSHL-m LID21179,LID21180 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqGfatAdult8wksJunctions Junctions Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Genital Fat Pad A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqFlobeAdult8wksJunctions FrontalLobe J adult-8wks FrontalLobe RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003064 3064 GSM1000562 Gingeras CSHL-m LID47081,LID47082 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqFlobeAdult8wksJunctions Junctions Adult 8 weeks Frontal Lobe 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Frontal Lobe A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqDuodAdult8wksJunctions Duodenum J adult-8wks Duodenum RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002521 2521 GSM900187 Gingeras CSHL-m LID20730,LID20731 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqDuodAdult8wksJunctions Junctions Adult 8 weeks Duodenum Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Duodenum A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCortexAdult8wksJunctions Cortex J adult-8wks Cortex RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003063 3063 GSM1000563 Gingeras CSHL-m LID47032,LID47033 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCortexAdult8wksJunctions Junctions Adult 8 weeks Cortex 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Cortex A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqColonAdult8wksJunctions Colon J adult-8wks Colon RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002512 2512 GSM900198 Gingeras CSHL-m LID21040,LID21041 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqColonAdult8wksJunctions Junctions Adult 8 weeks Colon Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Colon A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE18Junctions CNS E18 J E18 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003057 3057 GSM1000570 Gingeras CSHL-m LID46950,LID46951 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE18Junctions Junctions Embryonic day 18 Central Nervous System 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions CNS E18 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE14Junctions CNS E14 J E14 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003056 3056 GSM1000569 Gingeras CSHL-m LID46948,LID46949 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE14Junctions Junctions Embryonic day 14 Central Nervous System 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions CNS E14 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE11halfJunctions CNS E11.5 J E11.5 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003052 3052 GSM1000573 Gingeras CSHL-m LID46946,LID46947 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE11halfJunctions Junctions Embryonic day 11.5 Central Nervous System 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions CNS E11.5 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCbellumAdult8wksJunctions Cerebellum J adult-8wks Cerebellum RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003058 3058 GSM1000567 Gingeras CSHL-m LID47036,LID47037 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCbellumAdult8wksJunctions Junctions Adult 8 weeks Cerebellum 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Cerebellum A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqBladderAdult8wksJunctions Bladder J adult-8wks Bladder RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003062 3062 GSM1000564 Gingeras CSHL-m LID47030,LID47031 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqBladderAdult8wksJunctions Junctions Adult 8 weeks Urinary Bladder 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 Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Bladder A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqAdrenalAdult8wksJunctions Adrenal J adult-8wks Adrenal RnaSeq ENCODE Mar 2012 Freeze 2012-03-23 2012-12-23 wgEncodeEM002520 2520 GSM900188 Gingeras CSHL-m LID20728,LID20729 iIDR cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqAdrenalAdult8wksJunctions Junctions Adult 8 weeks Adrenal gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions Adrenal A8 Long RNA-seq Junctions from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqViewPlusRawSignal Plus Raw Signal Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression and Regulation 
wgEncodeCshlLongRnaSeqWbrainE14halfPlusRawRep2 WholeBrain + 2 E14.5 WholeBrain RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003055 3055 GSM1000572 Gingeras CSHL-m LID46988 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqWbrainE14halfPlusRawRep2 PlusRawSignal Embryonic day 14.5 Whole Brain 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Whole Brain E14.5 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqWbrainE14halfPlusRawRep1 WholeBrain + 1 E14.5 WholeBrain RnaSeq ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEM003055 3055 GSM1000572 Gingeras CSHL-m LID46987 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqWbrainE14halfPlusRawRep1 PlusRawSignal Embryonic day 14.5 Whole Brain 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Whole Brain E14.5 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqThymusAdult8wksPlusRawRep2 Thymus + 2 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2012-01-06 2012-10-05 wgEncodeEM002518 2518 GSM900192 Gingeras CSHL-m LID20923 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqThymusAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Thymus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Thymus A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqThymusAdult8wksPlusRawRep1 Thymus + 1 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002518 2518 GSM900192 Gingeras CSHL-m LID20922 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqThymusAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Thymus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Thymus A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqTestisAdult8wksPlusRawRep2 Testis + 2 adult-8wks Testis RnaSeq ENCODE Mar 2012 Freeze 2012-01-10 2012-10-10 wgEncodeEM002519 2519 GSM900193 Gingeras CSHL-m LID20869 cell 2x76D 2 longPolyA Illumina_GA2x M C57BL/6J wgEncodeCshlLongRnaSeqTestisAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Testis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Male A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Testis A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqTestisAdult8wksPlusRawRep1 Testis + 1 adult-8wks Testis RnaSeq ENCODE Mar 2012 Freeze 2012-01-06 2012-10-05 wgEncodeEM002519 2519 GSM900193 Gingeras CSHL-m LID20868 cell 2x76D 1 longPolyA Illumina_GA2x M C57BL/6J wgEncodeCshlLongRnaSeqTestisAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Testis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Male A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Testis A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSfatAdult8wksPlusRawRep2 SubcFatPad + 2 adult-8wks SubcFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002528 2528 GSM900191 Gingeras CSHL-m LID21182 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSfatAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Subcutaneous Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Subcutaneous Fat Pad A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSfatAdult8wksPlusRawRep1 SubcFatPad + 1 adult-8wks SubcFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002528 2528 GSM900191 Gingeras CSHL-m LID21181 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSfatAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Subcutaneous Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Subcutaneous Fat Pad A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqStomAdult8wksPlusRawRep2 Stomach + 2 adult-8wks Stomach RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002527 2527 GSM900185 Gingeras CSHL-m LID20733 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqStomAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Stomach Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Stomach A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqStomAdult8wksPlusRawRep1 Stomach + 1 adult-8wks Stomach RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002527 2527 GSM900185 Gingeras CSHL-m LID20732 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqStomAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Stomach Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Stomach A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSpleenAdult8wksPlusRawRep2 Spleen + 2 adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002517 2517 GSM900197 Gingeras CSHL-m LID21039 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSpleenAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Spleen Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Spleen A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSpleenAdult8wksPlusRawRep1 Spleen + 1 adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2012-01-06 2012-10-05 wgEncodeEM002517 2517 GSM900197 Gingeras CSHL-m LID21038 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSpleenAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Spleen Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Spleen A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSmintAdult8wksPlusRawRep2 SmInt + 2 adult-8wks SmIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002526 2526 GSM900186 Gingeras CSHL-m LID20820 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSmintAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Small Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Small Intestine A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSmintAdult8wksPlusRawRep1 SmInt + 1 adult-8wks SmIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002526 2526 GSM900186 Gingeras CSHL-m LID20819 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSmintAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Small Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Small Intestine A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqPlacAdult8wksPlusRawRep2 Placenta + 2 adult-8wks Placenta RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003061 3061 GSM1000565 Gingeras CSHL-m LID46984 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqPlacAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Placenta 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Placenta A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqPlacAdult8wksPlusRawRep1 Placenta + 1 adult-8wks Placenta RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003061 3061 GSM1000565 Gingeras CSHL-m LID46983 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqPlacAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Placenta 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Placenta A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqOvaryAdult8wksPlusRawRep2 Ovary + 2 adult-8wks Ovary RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002525 2525 GSM900183 Gingeras CSHL-m LID20822 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqOvaryAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Ovary Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Ovary A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqOvaryAdult8wksPlusRawRep1 Ovary + 1 adult-8wks Ovary RnaSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEM002525 2525 GSM900183 Gingeras CSHL-m LID20821 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqOvaryAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Ovary Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Ovary A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqMamgAdult8wksPlusRawRep2 MaGland + 2 adult-8wks MammaryGland RnaSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEM002524 2524 GSM900184 Gingeras CSHL-m LID20925 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqMamgAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Mammary Gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Mammary Gland A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqMamgAdult8wksPlusRawRep1 MaGland + 1 adult-8wks MammaryGland RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002524 2524 GSM900184 Gingeras CSHL-m LID20924 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqMamgAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Mammary Gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Mammary Gland A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLungAdult8wksPlusRawRep2 Lung + 2 adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002516 2516 GSM900196 Gingeras CSHL-m LID20921 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLungAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Lung Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Lung A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLungAdult8wksPlusRawRep1 Lung + 1 adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002516 2516 GSM900196 Gingeras CSHL-m LID20920 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLungAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Lung Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Lung A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE18PlusRawRep2 Liver E18 + 2 E18 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003060 3060 GSM1000566 Gingeras CSHL-m LID47149 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE18PlusRawRep2 PlusRawSignal Embryonic day 18 Liver 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Liver E18 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE18PlusRawRep1 Liver E18 + 1 E18 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003060 3060 GSM1000566 Gingeras CSHL-m LID47148 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE18PlusRawRep1 PlusRawSignal Embryonic day 18 Liver 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Liver E18 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14halfPlusRawRep2 Liver E14.5 + 2 E14.5 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003054 3054 GSM1000571 Gingeras CSHL-m LID47147 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14halfPlusRawRep2 PlusRawSignal Embryonic day 14.5 Liver 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Liver E14.5 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14halfPlusRawRep1 Liver E14.5 + 1 E14.5 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003054 3054 GSM1000571 Gingeras CSHL-m LID47146 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14halfPlusRawRep1 PlusRawSignal Embryonic day 14.5 Liver 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Liver E14.5 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14PlusRawRep2 Liver E14 + 2 E14 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003053 3053 GSM1000574 Gingeras CSHL-m LID47145 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14PlusRawRep2 PlusRawSignal Embryonic day 14 Liver 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Liver E14 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14PlusRawRep1 Liver E14 + 1 E14 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEM003053 3053 GSM1000574 Gingeras CSHL-m LID47144 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14PlusRawRep1 PlusRawSignal Embryonic day 14 Liver 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Liver E14 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverAdult8wksPlusRawRep2 Liver A8 + 2 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002515 2515 GSM900195 Gingeras CSHL-m LID21043 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLiverAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Liver Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Liver A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverAdult8wksPlusRawRep1 Liver A8 + 1 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002515 2515 GSM900195 Gingeras CSHL-m LID21042 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLiverAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Liver Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Liver A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLimbE14halfPlusRawRep2 Limb + 2 E14.5 Limb RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003059 3059 GSM1000568 Gingeras CSHL-m LID46986 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLimbE14halfPlusRawRep2 PlusRawSignal Embryonic day 14.5 Limb 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Limb E14.5 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLimbE14halfPlusRawRep1 Limb + 1 E14.5 Limb RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003059 3059 GSM1000568 Gingeras CSHL-m LID46985 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLimbE14halfPlusRawRep1 PlusRawSignal Embryonic day 14.5 Limb 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Limb E14.5 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLgintAdult8wksPlusRawRep2 LgInt + 2 adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002523 2523 GSM900189 Gingeras CSHL-m LID21184 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLgintAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Large Intestine A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLgintAdult8wksPlusRawRep1 LgInt + 1 adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002523 2523 GSM900189 Gingeras CSHL-m LID21183 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLgintAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Large Intestine A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqKidneyAdult8wksPlusRawRep2 Kidney + 2 adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2012-01-06 2012-10-05 wgEncodeEM002514 2514 GSM900194 Gingeras CSHL-m LID20873 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqKidneyAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Kidney Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Kidney A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqKidneyAdult8wksPlusRawRep1 Kidney + 1 adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002514 2514 GSM900194 Gingeras CSHL-m LID20872 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqKidneyAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Kidney Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Kidney A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqHeartAdult8wksPlusRawRep2 Heart + 2 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002513 2513 GSM900199 Gingeras CSHL-m LID20871 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqHeartAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Heart Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Heart A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqHeartAdult8wksPlusRawRep1 Heart + 1 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002513 2513 GSM900199 Gingeras CSHL-m LID20870 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqHeartAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Heart Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Heart A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqGfatAdult8wksPlusRawRep2 GenFatPad + 2 adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002522 2522 GSM900190 Gingeras CSHL-m LID21180 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqGfatAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Genital Fat Pad A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqGfatAdult8wksPlusRawRep1 GenFatPad + 1 adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002522 2522 GSM900190 Gingeras CSHL-m LID21179 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqGfatAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Genital Fat Pad A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqFlobeAdult8wksPlusRawRep2 FrontalLobe + 2 adult-8wks FrontalLobe RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003064 3064 GSM1000562 Gingeras CSHL-m LID47082 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqFlobeAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Frontal Lobe 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Frontal Lobe A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqFlobeAdult8wksPlusRawRep1 FrontalLobe + 1 adult-8wks FrontalLobe RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003064 3064 GSM1000562 Gingeras CSHL-m LID47081 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqFlobeAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Frontal Lobe 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Frontal Lobe A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqDuodAdult8wksPlusRawRep2 Duodenum + 2 adult-8wks Duodenum RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002521 2521 GSM900187 Gingeras CSHL-m LID20731 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqDuodAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Duodenum Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Duodenum A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqDuodAdult8wksPlusRawRep1 Duodenum + 1 adult-8wks Duodenum RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002521 2521 GSM900187 Gingeras CSHL-m LID20730 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqDuodAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Duodenum Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Duodenum A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep2 Cortex + 2 adult-8wks Cortex RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003063 3063 GSM1000563 Gingeras CSHL-m LID47033 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Cortex 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Cortex A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep1 Cortex + 1 adult-8wks Cortex RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003063 3063 GSM1000563 Gingeras CSHL-m LID47032 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Cortex 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Cortex A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqColonAdult8wksPlusRawRep2 Colon + 2 adult-8wks Colon RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002512 2512 GSM900198 Gingeras CSHL-m LID21041 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqColonAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Colon Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Colon A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqColonAdult8wksPlusRawRep1 Colon + 1 adult-8wks Colon RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002512 2512 GSM900198 Gingeras CSHL-m LID21040 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqColonAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Colon Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Colon A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE18PlusRawRep2 CNS E18 + 2 E18 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003057 3057 GSM1000570 Gingeras CSHL-m LID46951 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE18PlusRawRep2 PlusRawSignal Embryonic day 18 Central Nervous System 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand CNS E18 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE18PlusRawRep1 CNS E18 + 1 E18 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003057 3057 GSM1000570 Gingeras CSHL-m LID46950 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE18PlusRawRep1 PlusRawSignal Embryonic day 18 Central Nervous System 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand CNS E18 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE14PlusRawRep2 CNS E14 + 2 E14 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003056 3056 GSM1000569 Gingeras CSHL-m LID46949 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE14PlusRawRep2 PlusRawSignal Embryonic day 14 Central Nervous System 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand CNS E14 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE14PlusRawRep1 CNS E14 + 1 E14 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003056 3056 GSM1000569 Gingeras CSHL-m LID46948 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE14PlusRawRep1 PlusRawSignal Embryonic day 14 Central Nervous System 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand CNS E14 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE11halfPlusRawRep2 CNS E11.5 + 2 E11.5 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEM003052 3052 GSM1000573 Gingeras CSHL-m LID46947 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE11halfPlusRawRep2 PlusRawSignal Embryonic day 11.5 Central Nervous System 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand CNS E11.5 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE11halfPlusRawRep1 CNS E11.5 + 1 E11.5 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003052 3052 GSM1000573 Gingeras CSHL-m LID46946 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE11halfPlusRawRep1 PlusRawSignal Embryonic day 11.5 Central Nervous System 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand CNS E11.5 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCbellumAdult8wksPlusRawRep2 Cerebellum + 2 adult-8wks Cerebellum RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003058 3058 GSM1000567 Gingeras CSHL-m LID47037 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCbellumAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Cerebellum 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Cerebellum A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCbellumAdult8wksPlusRawRep1 Cerebellum + 1 adult-8wks Cerebellum RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003058 3058 GSM1000567 Gingeras CSHL-m LID47036 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCbellumAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Cerebellum 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Cerebellum A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqBladderAdult8wksPlusRawRep2 Bladder + 2 adult-8wks Bladder RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003062 3062 GSM1000564 Gingeras CSHL-m LID47031 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqBladderAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Urinary Bladder 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Bladder A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqBladderAdult8wksPlusRawRep1 Bladder + 1 adult-8wks Bladder RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003062 3062 GSM1000564 Gingeras CSHL-m LID47030 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqBladderAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Urinary Bladder 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Bladder A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqAdrenalAdult8wksPlusRawRep2 Adrenal + 2 adult-8wks Adrenal RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002520 2520 GSM900188 Gingeras CSHL-m LID20729 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqAdrenalAdult8wksPlusRawRep2 PlusRawSignal Adult 8 weeks Adrenal gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Adrenal A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqAdrenalAdult8wksPlusRawRep1 Adrenal + 1 adult-8wks Adrenal RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002520 2520 GSM900188 Gingeras CSHL-m LID20728 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqAdrenalAdult8wksPlusRawRep1 PlusRawSignal Adult 8 weeks Adrenal gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand Adrenal A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqViewMinusRawSignal Minus Raw Signal Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression and Regulation 
wgEncodeCshlLongRnaSeqWbrainE14halfMinusRawRep2 WholeBrain - 2 E14.5 WholeBrain RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003055 3055 GSM1000572 Gingeras CSHL-m LID46988 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqWbrainE14halfMinusRawRep2 MinusRawSignal Embryonic day 14.5 Whole Brain 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Whole Brain E14.5 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqWbrainE14halfMinusRawRep1 WholeBrain - 1 E14.5 WholeBrain RnaSeq ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEM003055 3055 GSM1000572 Gingeras CSHL-m LID46987 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqWbrainE14halfMinusRawRep1 MinusRawSignal Embryonic day 14.5 Whole Brain 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Whole Brain E14.5 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqThymusAdult8wksMinusRawRep2 Thymus - 2 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2012-01-06 2012-10-05 wgEncodeEM002518 2518 GSM900192 Gingeras CSHL-m LID20923 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqThymusAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Thymus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Thymus A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqThymusAdult8wksMinusRawRep1 Thymus - 1 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002518 2518 GSM900192 Gingeras CSHL-m LID20922 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqThymusAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Thymus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Thymus A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqTestisAdult8wksMinusRawRep2 Testis - 2 adult-8wks Testis RnaSeq ENCODE Mar 2012 Freeze 2012-01-10 2012-10-10 wgEncodeEM002519 2519 GSM900193 Gingeras CSHL-m LID20869 cell 2x76D 2 longPolyA Illumina_GA2x M C57BL/6J wgEncodeCshlLongRnaSeqTestisAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Testis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Male A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Testis A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqTestisAdult8wksMinusRawRep1 Testis - 1 adult-8wks Testis RnaSeq ENCODE Mar 2012 Freeze 2012-01-06 2012-10-05 wgEncodeEM002519 2519 GSM900193 Gingeras CSHL-m LID20868 cell 2x76D 1 longPolyA Illumina_GA2x M C57BL/6J wgEncodeCshlLongRnaSeqTestisAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Testis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Male A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Testis A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSfatAdult8wksMinusRawRep2 SubcFatPad - 2 adult-8wks SubcFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002528 2528 GSM900191 Gingeras CSHL-m LID21182 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSfatAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Subcutaneous Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Subcutaneous Fat Pad A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSfatAdult8wksMinusRawRep1 SubcFatPad - 1 adult-8wks SubcFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002528 2528 GSM900191 Gingeras CSHL-m LID21181 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSfatAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Subcutaneous Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Subcutaneous Fat Pad A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqStomAdult8wksMinusRawRep2 Stomach - 2 adult-8wks Stomach RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002527 2527 GSM900185 Gingeras CSHL-m LID20733 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqStomAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Stomach Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Stomach A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqStomAdult8wksMinusRawRep1 Stomach - 1 adult-8wks Stomach RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002527 2527 GSM900185 Gingeras CSHL-m LID20732 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqStomAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Stomach Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Stomach A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSpleenAdult8wksMinusRawRep2 Spleen - 2 adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002517 2517 GSM900197 Gingeras CSHL-m LID21039 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSpleenAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Spleen Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Spleen A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSpleenAdult8wksMinusRawRep1 Spleen - 1 adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2012-01-06 2012-10-05 wgEncodeEM002517 2517 GSM900197 Gingeras CSHL-m LID21038 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSpleenAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Spleen Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Spleen A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSmintAdult8wksMinusRawRep2 SmInt - 2 adult-8wks SmIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002526 2526 GSM900186 Gingeras CSHL-m LID20820 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSmintAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Small Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Small Intestine A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSmintAdult8wksMinusRawRep1 SmInt - 1 adult-8wks SmIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002526 2526 GSM900186 Gingeras CSHL-m LID20819 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSmintAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Small Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Small Intestine A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqPlacAdult8wksMinusRawRep2 Placenta - 2 adult-8wks Placenta RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003061 3061 GSM1000565 Gingeras CSHL-m LID46984 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqPlacAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Placenta 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Placenta A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqPlacAdult8wksMinusRawRep1 Placenta - 1 adult-8wks Placenta RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003061 3061 GSM1000565 Gingeras CSHL-m LID46983 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqPlacAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Placenta 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Placenta A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqOvaryAdult8wksMinusRawRep2 Ovary - 2 adult-8wks Ovary RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002525 2525 GSM900183 Gingeras CSHL-m LID20822 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqOvaryAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Ovary Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Ovary A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqOvaryAdult8wksMinusRawRep1 Ovary - 1 adult-8wks Ovary RnaSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEM002525 2525 GSM900183 Gingeras CSHL-m LID20821 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqOvaryAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Ovary Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Ovary A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqMamgAdult8wksMinusRawRep2 MaGland - 2 adult-8wks MammaryGland RnaSeq ENCODE Mar 2012 Freeze 2012-02-02 2012-11-02 wgEncodeEM002524 2524 GSM900184 Gingeras CSHL-m LID20925 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqMamgAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Mammary Gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Mammary Gland A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqMamgAdult8wksMinusRawRep1 MaGland - 1 adult-8wks MammaryGland RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002524 2524 GSM900184 Gingeras CSHL-m LID20924 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqMamgAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Mammary Gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Mammary Gland A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLungAdult8wksMinusRawRep2 Lung - 2 adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002516 2516 GSM900196 Gingeras CSHL-m LID20921 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLungAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Lung Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Lung A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLungAdult8wksMinusRawRep1 Lung - 1 adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002516 2516 GSM900196 Gingeras CSHL-m LID20920 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLungAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Lung Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Lung A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE18MinusRawRep2 Liver E18 - 2 E18 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003060 3060 GSM1000566 Gingeras CSHL-m LID47149 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE18MinusRawRep2 MinusRawSignal Embryonic day 18 Liver 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Liver E18 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE18MinusRawRep1 Liver E18 - 1 E18 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003060 3060 GSM1000566 Gingeras CSHL-m LID47148 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE18MinusRawRep1 MinusRawSignal Embryonic day 18 Liver 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Liver E18 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14halfMinusRawRep2 Liver E14.5 - 2 E14.5 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003054 3054 GSM1000571 Gingeras CSHL-m LID47147 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14halfMinusRawRep2 MinusRawSignal Embryonic day 14.5 Liver 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Liver E14.5 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14halfMinusRawRep1 Liver E14.5 - 1 E14.5 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003054 3054 GSM1000571 Gingeras CSHL-m LID47146 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14halfMinusRawRep1 MinusRawSignal Embryonic day 14.5 Liver 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Liver E14.5 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14MinusRawRep2 Liver E14 - 2 E14 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003053 3053 GSM1000574 Gingeras CSHL-m LID47145 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14MinusRawRep2 MinusRawSignal Embryonic day 14 Liver 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Liver E14 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14MinusRawRep1 Liver E14 - 1 E14 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEM003053 3053 GSM1000574 Gingeras CSHL-m LID47144 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14MinusRawRep1 MinusRawSignal Embryonic day 14 Liver 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Liver E14 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverAdult8wksMinusRawRep2 Liver A8 - 2 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002515 2515 GSM900195 Gingeras CSHL-m LID21043 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLiverAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Liver Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Liver A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverAdult8wksMinusRawRep1 Liver A8 - 1 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002515 2515 GSM900195 Gingeras CSHL-m LID21042 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLiverAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Liver Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Liver A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLimbE14halfMinusRawRep2 Limb - 2 E14.5 Limb RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003059 3059 GSM1000568 Gingeras CSHL-m LID46986 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLimbE14halfMinusRawRep2 MinusRawSignal Embryonic day 14.5 Limb 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Limb E14.5 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLimbE14halfMinusRawRep1 Limb - 1 E14.5 Limb RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003059 3059 GSM1000568 Gingeras CSHL-m LID46985 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLimbE14halfMinusRawRep1 MinusRawSignal Embryonic day 14.5 Limb 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Limb E14.5 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLgintAdult8wksMinusRawRep2 LgInt - 2 adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002523 2523 GSM900189 Gingeras CSHL-m LID21184 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLgintAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Large Intestine A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLgintAdult8wksMinusRawRep1 LgInt - 1 adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002523 2523 GSM900189 Gingeras CSHL-m LID21183 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLgintAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Large Intestine A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqKidneyAdult8wksMinusRawRep2 Kidney - 2 adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2012-01-06 2012-10-05 wgEncodeEM002514 2514 GSM900194 Gingeras CSHL-m LID20873 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqKidneyAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Kidney Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Kidney A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqKidneyAdult8wksMinusRawRep1 Kidney - 1 adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002514 2514 GSM900194 Gingeras CSHL-m LID20872 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqKidneyAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Kidney Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Kidney A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqHeartAdult8wksMinusRawRep2 Heart - 2 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002513 2513 GSM900199 Gingeras CSHL-m LID20871 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqHeartAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Heart Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Heart A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqHeartAdult8wksMinusRawRep1 Heart - 1 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002513 2513 GSM900199 Gingeras CSHL-m LID20870 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqHeartAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Heart Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Heart A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqGfatAdult8wksMinusRawRep2 GenFatPad - 2 adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002522 2522 GSM900190 Gingeras CSHL-m LID21180 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqGfatAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Genital Fat Pad A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqGfatAdult8wksMinusRawRep1 GenFatPad - 1 adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002522 2522 GSM900190 Gingeras CSHL-m LID21179 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqGfatAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Genital Fat Pad A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqFlobeAdult8wksMinusRawRep2 FrontalLobe - 2 adult-8wks FrontalLobe RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003064 3064 GSM1000562 Gingeras CSHL-m LID47082 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqFlobeAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Frontal Lobe 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Frontal Lobe A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqFlobeAdult8wksMinusRawRep1 FrontalLobe - 1 adult-8wks FrontalLobe RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003064 3064 GSM1000562 Gingeras CSHL-m LID47081 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqFlobeAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Frontal Lobe 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Frontal Lobe A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqDuodAdult8wksMinusRawRep2 Duodenum - 2 adult-8wks Duodenum RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002521 2521 GSM900187 Gingeras CSHL-m LID20731 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqDuodAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Duodenum Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Duodenum A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqDuodAdult8wksMinusRawRep1 Duodenum - 1 adult-8wks Duodenum RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002521 2521 GSM900187 Gingeras CSHL-m LID20730 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqDuodAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Duodenum Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Duodenum A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep2 Cortex - 2 adult-8wks Cortex RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003063 3063 GSM1000563 Gingeras CSHL-m LID47033 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Cortex 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Cortex A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep1 Cortex - 1 adult-8wks Cortex RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003063 3063 GSM1000563 Gingeras CSHL-m LID47032 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Cortex 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Cortex A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqColonAdult8wksMinusRawRep2 Colon - 2 adult-8wks Colon RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002512 2512 GSM900198 Gingeras CSHL-m LID21041 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqColonAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Colon Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Colon A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqColonAdult8wksMinusRawRep1 Colon - 1 adult-8wks Colon RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002512 2512 GSM900198 Gingeras CSHL-m LID21040 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqColonAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Colon Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Colon A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE18MinusRawRep2 CNS E18  - 2 E18 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003057 3057 GSM1000570 Gingeras CSHL-m LID46951 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE18MinusRawRep2 MinusRawSignal Embryonic day 18 Central Nervous System 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand CNS E18 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE18MinusRawRep1 CNS E18 - 1 E18 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003057 3057 GSM1000570 Gingeras CSHL-m LID46950 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE18MinusRawRep1 MinusRawSignal Embryonic day 18 Central Nervous System 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand CNS E18 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE14MinusRawRep2 CNS E14 - 2 E14 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003056 3056 GSM1000569 Gingeras CSHL-m LID46949 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE14MinusRawRep2 MinusRawSignal Embryonic day 14 Central Nervous System 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand CNS E14 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE14MinusRawRep1 CNS E14 - 1 E14 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003056 3056 GSM1000569 Gingeras CSHL-m LID46948 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE14MinusRawRep1 MinusRawSignal Embryonic day 14 Central Nervous System 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand CNS E14 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE11halfMinusRawRep2 CNS E11.5 - 2 E11.5 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEM003052 3052 GSM1000573 Gingeras CSHL-m LID46947 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE11halfMinusRawRep2 MinusRawSignal Embryonic day 11.5 Central Nervous System 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand CNS E11.5 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE11halfMinusRawRep1 CNS E11.5 - 1 E11.5 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003052 3052 GSM1000573 Gingeras CSHL-m LID46946 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE11halfMinusRawRep1 MinusRawSignal Embryonic day 11.5 Central Nervous System 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand CNS E11.5 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCbellumAdult8wksMinusRawRep2 Cerebellum - 2 adult-8wks Cerebellum RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003058 3058 GSM1000567 Gingeras CSHL-m LID47037 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCbellumAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Cerebellum 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Cerebellum A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCbellumAdult8wksMinusRawRep1 Cerebellum - 1 adult-8wks Cerebellum RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003058 3058 GSM1000567 Gingeras CSHL-m LID47036 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCbellumAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Cerebellum 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Cerebellum A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqBladderAdult8wksMinusRawRep2 Bladder - 2 adult-8wks Bladder RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003062 3062 GSM1000564 Gingeras CSHL-m LID47031 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqBladderAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Urinary Bladder 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Bladder A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqBladderAdult8wksMinusRawRep1 Bladder - 1 adult-8wks Bladder RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003062 3062 GSM1000564 Gingeras CSHL-m LID47030 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqBladderAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Urinary Bladder 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 Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Bladder A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqAdrenalAdult8wksMinusRawRep2 Adrenal - 2 adult-8wks Adrenal RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002520 2520 GSM900188 Gingeras CSHL-m LID20729 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqAdrenalAdult8wksMinusRawRep2 MinusRawSignal Adult 8 weeks Adrenal gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Adrenal A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqAdrenalAdult8wksMinusRawRep1 Adrenal - 1 adult-8wks Adrenal RnaSeq ENCODE Mar 2012 Freeze 2012-02-01 2012-11-01 wgEncodeEM002520 2520 GSM900188 Gingeras CSHL-m LID20728 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqAdrenalAdult8wksMinusRawRep1 MinusRawSignal Adult 8 weeks Adrenal gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand Adrenal A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqViewContigs Contigs Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression and Regulation 
wgEncodeCshlLongRnaSeqWbrainE14halfContigs WholeBrain C E14.5 WholeBrain RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003055 3055 GSM1000572 Gingeras CSHL-m LID46987,LID46988 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqWbrainE14halfContigs Contigs Embryonic day 14.5 Whole Brain 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 Unknown A substrain of C57BL/6 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). Whole Brain E14.5 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqThymusAdult8wksContigs Thymus C adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002518 2518 GSM900192 Gingeras CSHL-m LID20922,LID20923 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqThymusAdult8wksContigs Contigs Adult 8 weeks Thymus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Thymus A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqTestisAdult8wksContigs Testis C adult-8wks Testis RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002519 2519 GSM900193 Gingeras CSHL-m LID20868,LID20869 cell 2x76D longPolyA Illumina_GA2x M C57BL/6J wgEncodeCshlLongRnaSeqTestisAdult8wksContigs Contigs Adult 8 weeks Testis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Male A substrain of C57BL/6 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). Testis A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSfatAdult8wksContigs SubcFatPad C adult-8wks SubcFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002528 2528 GSM900191 Gingeras CSHL-m LID21181,LID21182 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSfatAdult8wksContigs Contigs Adult 8 weeks Subcutaneous Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Subcutaneous Fat Pad A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqStomAdult8wksContigs Stomach C adult-8wks Stomach RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002527 2527 GSM900185 Gingeras CSHL-m LID20732,LID20733 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqStomAdult8wksContigs Contigs Adult 8 weeks Stomach Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Stomach A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSpleenAdult8wksContigs Spleen C adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002517 2517 GSM900197 Gingeras CSHL-m LID21038,LID21039 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSpleenAdult8wksContigs Contigs Adult 8 weeks Spleen Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Spleen A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSmintAdult8wksContigs SmInt C adult-8wks SmIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002526 2526 GSM900186 Gingeras CSHL-m LID20819,LID20820 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSmintAdult8wksContigs Contigs Adult 8 weeks Small Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Small Intestine A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqPlacAdult8wksContigs Placenta C adult-8wks Placenta RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003061 3061 GSM1000565 Gingeras CSHL-m LID46983,LID46984 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqPlacAdult8wksContigs Contigs Adult 8 weeks Placenta 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 Unknown A substrain of C57BL/6 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). Placenta A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqOvaryAdult8wksContigs Ovary C adult-8wks Ovary RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002525 2525 GSM900183 Gingeras CSHL-m LID20821,LID20822 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqOvaryAdult8wksContigs Contigs Adult 8 weeks Ovary Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Ovary A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqMamgAdult8wksContigs MaGland C adult-8wks MammaryGland RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002524 2524 GSM900184 Gingeras CSHL-m LID20924,LID20925 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqMamgAdult8wksContigs Contigs Adult 8 weeks Mammary Gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Mammary Gland A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLungAdult8wksContigs Lung C adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002516 2516 GSM900196 Gingeras CSHL-m LID20920,LID20921 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLungAdult8wksContigs Contigs Adult 8 weeks Lung Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Lung A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE18Contigs Liver E18 C E18 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003060 3060 GSM1000566 Gingeras CSHL-m LID47148,LID47149 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE18Contigs Contigs Embryonic day 18 Liver 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 Unknown A substrain of C57BL/6 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). Liver E18 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14halfContigs Liver E14.5 C E14.5 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEM003054 3054 GSM1000571 Gingeras CSHL-m LID47146,LID47147 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14halfContigs Contigs Embryonic day 14.5 Liver 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 Unknown A substrain of C57BL/6 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). Liver E14.5 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14Contigs Liver E14 C E14 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003053 3053 GSM1000574 Gingeras CSHL-m LID47144,LID47145 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14Contigs Contigs Embryonic day 14 Liver 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 Unknown A substrain of C57BL/6 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). Liver E14 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverAdult8wksContigs Liver A8 C adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002515 2515 GSM900195 Gingeras CSHL-m LID21042,LID21043 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLiverAdult8wksContigs Contigs Adult 8 weeks Liver Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Liver A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLimbE14halfContigs Limb C E14.5 Limb RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003059 3059 GSM1000568 Gingeras CSHL-m LID46985,LID46986 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLimbE14halfContigs Contigs Embryonic day 14.5 Limb 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 Unknown A substrain of C57BL/6 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). Limb E14.5 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLgintAdult8wksContigs LgInt C adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002523 2523 GSM900189 Gingeras CSHL-m LID21183,LID21184 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLgintAdult8wksContigs Contigs Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Large Intestine A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqKidneyAdult8wksContigs Kidney C adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002514 2514 GSM900194 Gingeras CSHL-m LID20872,LID20873 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqKidneyAdult8wksContigs Contigs Adult 8 weeks Kidney Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Kidney A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqHeartAdult8wksContigs Heart C adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002513 2513 GSM900199 Gingeras CSHL-m LID20870,LID20871 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqHeartAdult8wksContigs Contigs Adult 8 weeks Heart Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Heart A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqGfatAdult8wksContigs GenFatPad C adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002522 2522 GSM900190 Gingeras CSHL-m LID21179,LID21180 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqGfatAdult8wksContigs Contigs Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Genital Fat Pad A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqFlobeAdult8wksContigs FrontalLobe  C adult-8wks FrontalLobe RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003064 3064 GSM1000562 Gingeras CSHL-m LID47081,LID47082 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqFlobeAdult8wksContigs Contigs Adult 8 weeks Frontal Lobe 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 Unknown A substrain of C57BL/6 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). Frontal Lobe A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqDuodAdult8wksContigs Duodenum C adult-8wks Duodenum RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002521 2521 GSM900187 Gingeras CSHL-m LID20730,LID20731 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqDuodAdult8wksContigs Contigs Adult 8 weeks Duodenum Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Duodenum A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCortexAdult8wksContigs Cortex C adult-8wks Cortex RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003063 3063 GSM1000563 Gingeras CSHL-m LID47032,LID47033 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCortexAdult8wksContigs Contigs Adult 8 weeks Cortex 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 Unknown A substrain of C57BL/6 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). Cortex A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqColonAdult8wksContigs Colon C adult-8wks Colon RnaSeq ENCODE Mar 2012 Freeze 2012-02-08 2012-11-08 wgEncodeEM002512 2512 GSM900198 Gingeras CSHL-m LID21040,LID21041 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqColonAdult8wksContigs Contigs Adult 8 weeks Colon Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Colon A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE18Contigs CNS E18 C E18 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003057 3057 GSM1000570 Gingeras CSHL-m LID46950,LID46951 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE18Contigs Contigs Embryonic day 18 Central Nervous System 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 Unknown A substrain of C57BL/6 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). CNS E18 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE14Contigs CNS E14 C E14 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003056 3056 GSM1000569 Gingeras CSHL-m LID46948,LID46949 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE14Contigs Contigs Embryonic day 14 Central Nervous System 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 Unknown A substrain of C57BL/6 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). CNS E14 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE11halfContigs CNS E11.5 C E11.5 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003052 3052 GSM1000573 Gingeras CSHL-m LID46946,LID46947 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE11halfContigs Contigs Embryonic day 11.5 Central Nervous System 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 Unknown A substrain of C57BL/6 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). CNS E11.5 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCbellumAdult8wksContigs Cerebellum C adult-8wks Cerebellum RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003058 3058 GSM1000567 Gingeras CSHL-m LID47036,LID47037 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCbellumAdult8wksContigs Contigs Adult 8 weeks Cerebellum 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 Unknown A substrain of C57BL/6 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). Cerebellum A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqBladderAdult8wksContigs Bladder C adult-8wks Bladder RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003062 3062 GSM1000564 Gingeras CSHL-m LID47030,LID47031 cell 2x101D longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqBladderAdult8wksContigs Contigs Adult 8 weeks Urinary Bladder 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 Unknown A substrain of C57BL/6 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). Bladder A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqAdrenalAdult8wksContigs Adrenal C adult-8wks Adrenal RnaSeq ENCODE Mar 2012 Freeze 2012-02-09 2012-11-09 wgEncodeEM002520 2520 GSM900188 Gingeras CSHL-m LID20728,LID20729 cell 2x76D longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqAdrenalAdult8wksContigs Contigs Adult 8 weeks Adrenal gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 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). Adrenal A8 Long RNA-seq Contigs from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqViewAlignments Alignments Long RNA-seq from ENCODE/Cold Spring Harbor Lab Expression and Regulation 
wgEncodeCshlLongRnaSeqWbrainE14halfAlnRep2 WholeBrain Aln 2 E14.5 WholeBrain RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003055 3055 Gingeras CSHL-m LID46988 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqWbrainE14halfAlnRep2 Alignments Embryonic day 14.5 Whole Brain 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Whole Brain E14.5 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqWbrainE14halfAlnRep1 WholeBrain Aln 1 E14.5 WholeBrain RnaSeq ENCODE Jul 2012 Freeze 2012-07-12 2013-04-12 wgEncodeEM003055 3055 Gingeras CSHL-m LID46987 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqWbrainE14halfAlnRep1 Alignments Embryonic day 14.5 Whole Brain 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Whole Brain E14.5 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqThymusAdult8wksAlnRep2V2 Thymus Aln 2 adult-8wks Thymus RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002518 2518 Gingeras CSHL-m LID20923 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqThymusAdult8wksAlnRep2V2 Alignments Adult 8 weeks Thymus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Thymus A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqThymusAdult8wksAlnRep1V2 Thymus Aln 1 adult-8wks Thymus RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002518 2518 Gingeras CSHL-m LID20922 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqThymusAdult8wksAlnRep1V2 Alignments Adult 8 weeks Thymus Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Thymus A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqTestisAdult8wksAlnRep2V2 Testis Aln 2 adult-8wks Testis RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002519 2519 Gingeras CSHL-m LID20869 cell 2x76D 2 longPolyA Illumina_GA2x M C57BL/6J wgEncodeCshlLongRnaSeqTestisAdult8wksAlnRep2V2 Alignments Adult 8 weeks Testis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Male A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Testis A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqTestisAdult8wksAlnRep1V2 Testis Aln 1 adult-8wks Testis RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002519 2519 Gingeras CSHL-m LID20868 cell 2x76D 1 longPolyA Illumina_GA2x M C57BL/6J wgEncodeCshlLongRnaSeqTestisAdult8wksAlnRep1V2 Alignments Adult 8 weeks Testis Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Male A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Testis A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSfatAdult8wksAlnRep2V2 SubcFatPad Aln 2 adult-8wks SubcFatPad RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002528 2528 Gingeras CSHL-m LID21182 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSfatAdult8wksAlnRep2V2 Alignments Adult 8 weeks Subcutaneous Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Subcutaneous Fat Pad A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSfatAdult8wksAlnRep1V2 SubcFatPad Aln 1 adult-8wks SubcFatPad RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002528 2528 Gingeras CSHL-m LID21181 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSfatAdult8wksAlnRep1V2 Alignments Adult 8 weeks Subcutaneous Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Subcutaneous Fat Pad A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqStomAdult8wksAlnRep2V2 Stomach Aln 2 adult-8wks Stomach RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002527 2527 Gingeras CSHL-m LID20733 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqStomAdult8wksAlnRep2V2 Alignments Adult 8 weeks Stomach Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Stomach A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqStomAdult8wksAlnRep1V2 Stomach Aln 1 adult-8wks Stomach RnaSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEM002527 2527 Gingeras CSHL-m LID20732 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqStomAdult8wksAlnRep1V2 Alignments Adult 8 weeks Stomach Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Stomach A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSplAdult8wksAlnRep2V2 Spleen Aln 2 adult-8wks Spleen RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002517 2517 Gingeras CSHL-m LID21039 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSplAdult8wksAlnRep2V2 Alignments Adult 8 weeks Spleen Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Spleen A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSplAdult8wksAlnRep1V2 Spleen Aln 1 adult-8wks Spleen RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002517 2517 Gingeras CSHL-m LID21038 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSplAdult8wksAlnRep1V2 Alignments Adult 8 weeks Spleen Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Spleen A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSmintAdult8wksAlnRep2V2 SmInt Aln 2 adult-8wks SmIntestine RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002526 2526 Gingeras CSHL-m LID20820 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSmintAdult8wksAlnRep2V2 Alignments Adult 8 weeks Small Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Small Intestine A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqSmintAdult8wksAlnRep1V2 SmInt Aln 1 adult-8wks SmIntestine RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002526 2526 Gingeras CSHL-m LID20819 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqSmintAdult8wksAlnRep1V2 Alignments Adult 8 weeks Small Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Small Intestine A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqPlacAdult8wksAlnRep2 Placenta Aln 2 adult-8wks Placenta RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003061 3061 Gingeras CSHL-m LID46984 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqPlacAdult8wksAlnRep2 Alignments Adult 8 weeks Placenta 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Placenta A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqPlacAdult8wksAlnRep1 Placenta Aln 1 adult-8wks Placenta RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003061 3061 Gingeras CSHL-m LID46983 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqPlacAdult8wksAlnRep1 Alignments Adult 8 weeks Placenta 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Placenta A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqOvaryAdult8wksAlnRep2V2 Ovary Aln 2 adult-8wks Ovary RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002525 2525 Gingeras CSHL-m LID20822 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqOvaryAdult8wksAlnRep2V2 Alignments Adult 8 weeks Ovary Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Ovary A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqOvaryAdult8wksAlnRep1V2 Ovary Aln 1 adult-8wks Ovary RnaSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEM002525 2525 Gingeras CSHL-m LID20821 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqOvaryAdult8wksAlnRep1V2 Alignments Adult 8 weeks Ovary Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Ovary A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqMamgAdult8wksAlnRep2V2 MaGland Aln 2 adult-8wks MammaryGland RnaSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEM002524 2524 Gingeras CSHL-m LID20925 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqMamgAdult8wksAlnRep2V2 Alignments Adult 8 weeks Mammary Gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Mammary Gland A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqMamgAdult8wksAlnRep1V2 MaGland Aln 1 adult-8wks MammaryGland RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002524 2524 Gingeras CSHL-m LID20924 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqMamgAdult8wksAlnRep1V2 Alignments Adult 8 weeks Mammary Gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Mammary Gland A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLungAdult8wksAlnRep2V2 Lung Aln 2 adult-8wks Lung RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002516 2516 Gingeras CSHL-m LID20921 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLungAdult8wksAlnRep2V2 Alignments Adult 8 weeks Lung Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Lung A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLungAdult8wksAlnRep1V2 Lung Aln 1 adult-8wks Lung RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002516 2516 Gingeras CSHL-m LID20920 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLungAdult8wksAlnRep1V2 Alignments Adult 8 weeks Lung Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Lung A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE18AlnRep2 Liver E18 Aln 2 E18 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003060 3060 Gingeras CSHL-m LID47149 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE18AlnRep2 Alignments Embryonic day 18 Liver 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Liver E18 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE18AlnRep1 Liver E18 Aln 1 E18 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003060 3060 Gingeras CSHL-m LID47148 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE18AlnRep1 Alignments Embryonic day 18 Liver 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Liver E18 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14halfAlnRep2 Liver E14.5 Aln 2 E14.5 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003054 3054 Gingeras CSHL-m LID47147 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14halfAlnRep2 Alignments Embryonic day 14.5 Liver 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Liver E14.5 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14halfAlnRep1 Liver E14.5 Aln 1 E14.5 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003054 3054 Gingeras CSHL-m LID47146 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14halfAlnRep1 Alignments Embryonic day 14.5 Liver 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Liver E14.5 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14AlnRep2 Liver E14 Aln 2 E14 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003053 3053 Gingeras CSHL-m LID47145 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14AlnRep2 Alignments Embryonic day 14 Liver 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Liver E14 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverE14AlnRep1 Liver E14 Aln 1 E14 Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEM003053 3053 Gingeras CSHL-m LID47144 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLiverE14AlnRep1 Alignments Embryonic day 14 Liver 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Liver E14 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverAdult8wksAlnRep2V2 Liver A8 Aln 2 adult-8wks Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEM002515 2515 Gingeras CSHL-m LID21043 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLiverAdult8wksAlnRep2V2 Alignments Adult 8 weeks Liver Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Liver A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLiverAdult8wksAlnRep1V2 Liver A8 Aln 1 adult-8wks Liver RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002515 2515 Gingeras CSHL-m LID21042 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLiverAdult8wksAlnRep1V2 Alignments Adult 8 weeks Liver Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Liver A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLimbE14halfAlnRep2 Limb Aln 2 E14.5 Limb RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003059 3059 Gingeras CSHL-m LID46986 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLimbE14halfAlnRep2 Alignments Embryonic day 14.5 Limb 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Limb E14.5 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLimbE14halfAlnRep1 Limb Aln 1 E14.5 Limb RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003059 3059 Gingeras CSHL-m LID46985 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqLimbE14halfAlnRep1 Alignments Embryonic day 14.5 Limb 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Limb E14.5 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLgintAdult8wksAlnRep2V2 LgInt Aln 2 adult-8wks LgIntestine RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002523 2523 Gingeras CSHL-m LID21184 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLgintAdult8wksAlnRep2V2 Alignments Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Large Intestine A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqLgintAdult8wksAlnRep1V2 LgInt Aln 1 adult-8wks LgIntestine RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002523 2523 Gingeras CSHL-m LID21183 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqLgintAdult8wksAlnRep1V2 Alignments Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Large Intestine A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqKidneyAdult8wksAlnRep2V2 Kidney Aln 2 adult-8wks Kidney RnaSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEM002514 2514 Gingeras CSHL-m LID20873 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqKidneyAdult8wksAlnRep2V2 Alignments Adult 8 weeks Kidney Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Kidney A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqKidneyAdult8wksAlnRep1V2 Kidney Aln 1 adult-8wks Kidney RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002514 2514 Gingeras CSHL-m LID20872 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqKidneyAdult8wksAlnRep1V2 Alignments Adult 8 weeks Kidney Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Kidney A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqHeartAdult8wksAlnRep2V2 Heart Aln 2 adult-8wks Heart RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002513 2513 Gingeras CSHL-m LID20871 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqHeartAdult8wksAlnRep2V2 Alignments Adult 8 weeks Heart Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Heart A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqHeartAdult8wksAlnRep1V2 Heart Aln 1 adult-8wks Heart RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002513 2513 Gingeras CSHL-m LID20870 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqHeartAdult8wksAlnRep1V2 Alignments Adult 8 weeks Heart Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Heart A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqGfatAdult8wksAlnRep2V2 GenFatPad Aln 2 adult-8wks GenitalFatPad RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002522 2522 Gingeras CSHL-m LID21180 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqGfatAdult8wksAlnRep2V2 Alignments Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Genital Fat Pad A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqGfatAdult8wksAlnRep1V2 GenFatPad Aln 1 adult-8wks GenitalFatPad RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002522 2522 Gingeras CSHL-m LID21179 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqGfatAdult8wksAlnRep1V2 Alignments Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Genital Fat Pad A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqFlobeAdult8wksAlnRep2 FrontalLobe Aln 2 adult-8wks FrontalLobe RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003064 3064 Gingeras CSHL-m LID47082 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqFlobeAdult8wksAlnRep2 Alignments Adult 8 weeks Frontal Lobe 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Frontal Lobe A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqFlobeAdult8wksAlnRep1 FrontalLobe Aln 1 adult-8wks FrontalLobe RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003064 3064 Gingeras CSHL-m LID47081 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqFlobeAdult8wksAlnRep1 Alignments Adult 8 weeks Frontal Lobe 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Frontal Lobe A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqDuodAdult8wksAlnRep2V2 Duodenum Aln 2 adult-8wks Duodenum RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002521 2521 Gingeras CSHL-m LID20731 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqDuodAdult8wksAlnRep2V2 Alignments Adult 8 weeks Duodenum Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Duodenum A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqDuodAdult8wksAlnRep1V2 Duodenum Aln 1 adult-8wks Duodenum RnaSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEM002521 2521 Gingeras CSHL-m LID20730 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqDuodAdult8wksAlnRep1V2 Alignments Adult 8 weeks Duodenum Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Duodenum A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCortexAdult8wksAlnRep2 Cortex Aln 2 adult-8wks Cortex RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003063 3063 Gingeras CSHL-m LID47033 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCortexAdult8wksAlnRep2 Alignments Adult 8 weeks Cortex 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Cortex A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCortexAdult8wksAlnRep1 Cortex Aln 1 adult-8wks Cortex RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003063 3063 Gingeras CSHL-m LID47032 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCortexAdult8wksAlnRep1 Alignments Adult 8 weeks Cortex 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Cortex A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqColonAdult8wksAlnRep2V2 Colon Aln 2 adult-8wks Colon RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002512 2512 Gingeras CSHL-m LID21041 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqColonAdult8wksAlnRep2V2 Alignments Adult 8 weeks Colon Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Colon A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqColonAdult8wksAlnRep1V2 Colon Aln 1 adult-8wks Colon RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002512 2512 Gingeras CSHL-m LID21040 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqColonAdult8wksAlnRep1V2 Alignments Adult 8 weeks Colon Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Colon A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE18AlnRep2 CNS E18 Aln 2 E18 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003057 3057 Gingeras CSHL-m LID46951 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE18AlnRep2 Alignments Embryonic day 18 Central Nervous System 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch CNS E18 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE18AlnRep1 CNS E18 Aln 1 E18 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003057 3057 Gingeras CSHL-m LID46950 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE18AlnRep1 Alignments Embryonic day 18 Central Nervous System 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch CNS E18 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE14AlnRep2 CNS E14 Aln 2 E14 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003056 3056 Gingeras CSHL-m LID46949 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE14AlnRep2 Alignments Embryonic day 14 Central Nervous System 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch CNS E14 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE14AlnRep1 CNS E14 Aln 1 E14 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003056 3056 Gingeras CSHL-m LID46948 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE14AlnRep1 Alignments Embryonic day 14 Central Nervous System 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch CNS E14 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE11halfAlnRep2 CNS E11.5 Aln 2 E11.5 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-11 2013-04-11 wgEncodeEM003052 3052 Gingeras CSHL-m LID46947 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE11halfAlnRep2 Alignments Embryonic day 11.5 Central Nervous System 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch CNS E11.5 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCnsE11halfAlnRep1 CNS E11.5 Aln 1 E11.5 CNS RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003052 3052 Gingeras CSHL-m LID46946 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCnsE11halfAlnRep1 Alignments Embryonic day 11.5 Central Nervous System 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch CNS E11.5 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCbellumAdult8wksAlnRep2 Cerebellum Aln 2 adult-8wks Cerebellum RnaSeq ENCODE Jul 2012 Freeze 2012-07-13 2013-04-13 wgEncodeEM003058 3058 Gingeras CSHL-m LID47037 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCbellumAdult8wksAlnRep2 Alignments Adult 8 weeks Cerebellum 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Cerebellum A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqCbellumAdult8wksAlnRep1 Cerebellum Aln 1 adult-8wks Cerebellum RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003058 3058 Gingeras CSHL-m LID47036 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqCbellumAdult8wksAlnRep1 Alignments Adult 8 weeks Cerebellum 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Cerebellum A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqBladderAdult8wksAlnRep2 Bladder Aln 2 adult-8wks Bladder RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-13 wgEncodeEM003062 3062 Gingeras CSHL-m LID47031 cell 2x101D 2 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqBladderAdult8wksAlnRep2 Alignments Adult 8 weeks Urinary Bladder 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Bladder A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqBladderAdult8wksAlnRep1 Bladder Aln 1 adult-8wks Bladder RnaSeq ENCODE Jul 2012 Freeze 2012-07-14 2013-04-14 wgEncodeEM003062 3062 Gingeras CSHL-m LID47030 cell 2x101D 1 longPolyA Illumina_HiSeq_2000 U C57BL/6J wgEncodeCshlLongRnaSeqBladderAdult8wksAlnRep1 Alignments Adult 8 weeks Urinary Bladder 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 Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Bladder A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep2V2 Adrenal Aln 2 adult-8wks Adrenal RnaSeq ENCODE Jul 2012 Freeze 2012-07-29 2013-04-29 wgEncodeEM002520 2520 Gingeras CSHL-m LID20729 cell 2x76D 2 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep2V2 Alignments Adult 8 weeks Adrenal gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Adrenal A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL Expression and Regulation 
wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep1V2 Adrenal Aln 1 adult-8wks Adrenal RnaSeq ENCODE Jul 2012 Freeze 2012-07-30 2013-04-29 wgEncodeEM002520 2520 Gingeras CSHL-m LID20728 cell 2x76D 1 longPolyA Illumina_GA2x U C57BL/6J wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep1V2 Alignments Adult 8 weeks Adrenal gland Sequencing analysis of RNA expression Gingeras Gingeras - Cold Spring Harbor Laboratory Whole cell Paired 76 nt directed reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer IIx Unknown A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch Adrenal A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL Expression and Regulation 
exoniphy Exoniphy Exoniphy Mouse/Rat/Human/Dog Genes and Gene Predictions Description The exoniphy program identifies evolutionarily conserved protein-coding exons in a multiple alignment using a phylogenetic hidden Markov model (phylo-HMM), a statistical model that simultaneously describes exon structure and exon evolution. This track shows exoniphy predictions for the human Mar. 2006 (hg18), mouse Feb. 2006 (mm8), rat Nov. 2004 (rn4), and dog May 2005 (canFam2) genomes, as aligned by the multiz program. For this track, only alignments on the &quot;syntenic net&quot; between human and each other species were considered. The predictions for mouse Feb. 2006 (mm8) were lifted to the mouse Jul. 2007 (mm9) genome. Methods For a description of exoniphy, see Siepel et al. (2004). Multiz is described in Blanchette et al. (2004). The alignment chaining methods behind the &quot;syntenic net&quot; are described in Kent et al. (2003). Acknowledgments Thanks to Brona Brejova of Cornell University for producing these predictions. References Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Siepel A, Haussler D. Computational identification of evolutionarily conserved exons. Proc. 8th Int'l Conf. on Research in Computational Molecular Biology, 177-186 (2004). 
FaceBase24SampleTypesAvg FaceBase 24STypes FaceBase 24 Sample Types Averaged Expression and Regulation Description This dataset represents 24 independent samples of different regions of developing craniofacial structures obtained from embryonic day 8.5, 9.5, 10.5, and 11.5 mouse embryos. RNA was prepared separately from each sample and subjected to a custom mRNA microlabeling protocol so as to allow for hybridization to individual Affymetrix Mouse Genes 1.0 ST Arrays. The various samples correspond to independent replicates from the following cell types: e8.5 Paraxial Mesodem e8.5 Floor Plate Neural Epithelium e8.5 Hindbrain Neural Epithelium e8.5 Non-floor Plate Neural Epithelium e9.5 Olfactory Placode e9.5 Otic Vesicle e9.5 Facial Mesenchyme e9.5 Mandibular Arch e9.5 Maxillary Arch e9.5 Neural Epithelium e10.5 Rathke's Pouch e10.5 Nasal Pit e10.5 Mandibular Arch e10.5 Maxillary Arch e10.5 Mandibular Columnar Epithelium e10.5 Maxillary Columnar Epithelium e10.5 Lateral Nasal Process e10.5 Medial Nasal Process e10.5 Central Neural Epithelium e10.5 Flanking Neural Epithelium e10.5 Lateral Eminence Neural Epithelium e10.5 Medial Eminence Neural Epithelium e11.5 Medial Nasal Prominence Display Conventions In dense mode, the track color denotes the average signal over all experiments on a log base 2 scale. Lighter colors correspond to lower signals and darker colors correspond to higher signals. In full mode, the color of each item represents the log base 2 ratio of the signal of that particular experiment to the median signal of all experiments for that probe. Methods Microarry data was subjected to RMA normalization and individual gene expression levels per probeset per sample were expressed as a ratio relative to the level of that probeset's expression using whole Postnatal day 1 mouse RNA as a universal reference. Colored blocks extend over the length of the corresponding gene and depict expression in the craniofacial sample relative to that in the reference RNA sample. Credits This track was created with the help of the following people: Dissections, RNA purification, and labeling were carried out by Eric Brunskill and Steven Potter. Hybridization and processing by Sean Smith and Hung-Chi Liang in the Cincinnati Children's Hospital gene expression analysis core. Data was analyzed and transformed into UCSC genome browser array format by Andrew Plassard and Bruce Aronow. This work was part of the Global Gene Expression Atlas of Craniofacial Development project being carried out by the Facebase Consortium. Contact: &#66;&#114;&#117;&#99;e.&#65;&#114;&#111;n&#111;&#119;&#64;&#99;&#99;&#104;m&#99;.&#111;&#114;g References Brunskill EW, Potter AS, Distasio A, Dexheimer P, Plassard A, Aronow BJ, Potter SS. A gene expression atlas of early craniofacial development. Dev Biol. 2014 Jul 15;391(2):133-46. PMID: 24780627 
wgEncodeFsuRepliChip FSU Repli-chip Replication Timing by Repli-chip from ENCODE/FSU Expression and Regulation Description This track was produced as part of the ENCODE Project. This track shows genome-wide assessment of DNA replication timing in cell lines using NimbleGen tiling CGH microarrays. Each experiment represents the relative enrichment of early vs. late S-phase nascent strands in a given cell line, with data represented as a loess-smoothed function of individual timing values at probes spaced at even intervals across the genome. Regions with high values indicate domains of early replication where initiaion occurs earlier in S-phase or early in a higher proportion of cells. Display Conventions and Configuration Wavelet-smoothed Signal Wavelet-smoothed of mean early/late S-phase ratios. 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. Methods for replication timing profile creation and analysis are described in detail in Hiratani et al. (2008) and Ryba et al. (June 2011). Methods for individual stages are summarized below: Extraction protocol Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays. Replication intermediates were prepared from cells that were first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Hybridization protocol The hydridization set used the NimbleGen standard protocol. Cy3- and Cy5-labeled DNA samples (6 &micro;g each) were co-hybridized to Nimblegen CGH arrays containing evenly-spaced oligonucleotide probes across the mouse genome, with a median probe spacing of 1.1-5.8 kb. No differences in smoothed data have been detected with probe densities from 100 bp to 5.8 kb. Scan protocol NimbleGen MS 200 2 &micro;m resolution scanner and GenePix software were used per NimbleGen's standard protocol. Data processing NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e., from .pair files) from two independent biological replicates in which early- and late-replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and then averaged (limma package, R/Bioconductor). The mean early/late ratios were used to generate a smoothed profile (i.e., processed data) using local polynomial smoothing (loess, 300 kb span) for each chromosome using basic functions in the statistical language R. Verification Technical data quality was assessed by verifying high auto-correlation between neighboring timing values. Biological identity was confirmed by verifying consistent early or late replication by PCR at individual loci, as well as uniformity in replication profiles between replicate experiments. Credits These data were generated by the FSU ENCODE group. Contact: David M. Gilbert References Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B, Fussner E, Bazett-Jones DP, Plath K, Dalton S et al. Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res. 2010 Feb;20(2):155-69. Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, Lyou Y, Townes TM, Sch&#252;beler D, Gilbert DM. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 Oct 7;6(10):e245. Pope BD, Tsumagari K, Battaglia D, Ryba T, Hiratani I, Ehrlich M, Gilbert DM. DNA replication timing is maintained genome-wide in primary human myoblasts independent of D4Z4 contraction in FSH muscular dystrophy. PLoS One. 2011;6(11):e27413. Ryba T, Battaglia D, Pope BD, Hiratani I, Gilbert DM. Genome-scale analysis of replication timing: from bench to bioinformatics. Nat Protoc. 2011 Jun;6(6):870-95. Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Schulz TC, Robins AJ, Dalton S, Gilbert DM. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res. 2010 Jun;20(6):761-70. Ryba T, Hiratani I, Sasaki T, Battaglia D, Kulik M, Zhang J, Dalton S, Gilbert DM. Replication timing: a fingerprint for cell identity and pluripotency. PLoS Comput Biol. 2011 Oct;7(10):e1002225. 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. 
wgEncodeFsuRepliChipMelMWaveSignalRep2 MEL Ws 2 immortalized MEL RepliChip ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002975 2975 Gilbert FSU-m MEL_R2 GPL10989 2 M Unknown wgEncodeFsuRepliChipMelMWaveSignalRep2 None WaveSignal Immortal cells Leukemia (K562 analog) Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University NimbleGen Mouse CGH 3x720K Whole-Genome Tiling (FSU) Male Unknown strain origin Shows smoothed wavelet over all phases MEL Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipMelMWaveSignalRep1 MEL Ws 1 immortalized MEL RepliChip ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002975 2975 Gilbert FSU-m MEL_R1 GPL10989 1 M Unknown wgEncodeFsuRepliChipMelMWaveSignalRep1 None WaveSignal Immortal cells Leukemia (K562 analog) Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University NimbleGen Mouse CGH 3x720K Whole-Genome Tiling (FSU) Male Unknown strain origin Shows smoothed wavelet over all phases MEL Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipMefMWaveSignalRep1 MEF Ws 1 ageUnknown MEF RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002974 2974 Gilbert FSU-m MEF_R1 GPL9156 1 M Unknown wgEncodeFsuRepliChipMefMWaveSignalRep1 None WaveSignal the age when the real age is unknown Mouse Embryonic Fibroblast Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Unknown strain origin Shows smoothed wavelet over all phases MEF Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipL1210FWaveSignalRep2 L1210 Ws 2 immortalized L1210 RepliChip ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002973 2973 Gilbert FSU-m L1210_R2 GPL9156 2 F DBA/2 wgEncodeFsuRepliChipL1210FWaveSignalRep2 None WaveSignal Immortal cells lymphoblast from 8 month female Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Female Inbred strain used for Coat Color Experiments. Was DBA/212 but reclassified as DBA/2 Shows smoothed wavelet over all phases L1210 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipL1210FWaveSignalRep1 L1210 Ws 1 immortalized L1210 RepliChip ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002973 2973 Gilbert FSU-m L1210_R1 GPL9156 1 F DBA/2 wgEncodeFsuRepliChipL1210FWaveSignalRep1 None WaveSignal Immortal cells lymphoblast from 8 month female Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Female Inbred strain used for Coat Color Experiments. Was DBA/212 but reclassified as DBA/2 Shows smoothed wavelet over all phases L1210 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipJ185aUWaveSignalRep2 J185a Ws 2 immortalized J185a RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEM002979 2979 Gilbert FSU-m GPL9156 2 U Unknown wgEncodeFsuRepliChipJ185aUWaveSignalRep2 None WaveSignal Immortal cells Fetal myoblast Desmin+ Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Unknown Unknown strain origin Shows smoothed wavelet over all phases J185a Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipJ185aUWaveSignalRep1 J185a Ws 1 immortalized J185a RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEM002979 2979 Gilbert FSU-m GPL9156 1 U Unknown wgEncodeFsuRepliChipJ185aUWaveSignalRep1 None WaveSignal Immortal cells Fetal myoblast Desmin+ Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Unknown Unknown strain origin Shows smoothed wavelet over all phases J185a Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEstt2MWaveSignalRep2 ES-TT2 Ws 2 E0 ES-TT2 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEM002970 2970 Gilbert FSU-m ES-TT2_R2 GPL9156 2 M B6CBAF1/J wgEncodeFsuRepliChipEstt2MWaveSignalRep2 None WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from C57BL/6xCBA Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Derived from cross between C57BL/6J Female x CBA/J Male (C57BL/6 x CBA)F1/J. Shows smoothed wavelet over all phases ES-TT2 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEstt2MWaveSignalRep1 ES-TT2 Ws 1 E0 ES-TT2 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002970 2970 Gilbert FSU-m ES-TT2_R1 GPL9156 1 M B6CBAF1/J wgEncodeFsuRepliChipEstt2MWaveSignalRep1 None WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from C57BL/6xCBA Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Derived from cross between C57BL/6J Female x CBA/J Male (C57BL/6 x CBA)F1/J. Shows smoothed wavelet over all phases ES-TT2 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEstt2MDifff9dWaveSignalRep2 ES-TT2 NP Ws 2 E0 ES-TT2 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002969 2969 Gilbert FSU-m NP-TT2_R2 GPL9156 2 M B6CBAF1/J wgEncodeFsuRepliChipEstt2MDifff9dWaveSignalRep2 diffProtF_9d WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from C57BL/6xCBA Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Derived from cross between C57BL/6J Female x CBA/J Male (C57BL/6 x CBA)F1/J. 9 day differentiation of ES-TT2 cells in adherent monolayer culture (Gilbert) Shows smoothed wavelet over all phases ES-TT2 NP 9 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEstt2MDifff9dWaveSignalRep1 ES-TT2 NP Ws 1 E0 ES-TT2 RepliChip ENCODE Jul 2012 Freeze 2012-06-28 2012-03-31 2012-12-30 wgEncodeEM002969 2969 Gilbert FSU-m NP-TT2_R1 GPL9156 1 M B6CBAF1/J wgEncodeFsuRepliChipEstt2MDifff9dWaveSignalRep1 diffProtF_9d WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from C57BL/6xCBA Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Derived from cross between C57BL/6J Female x CBA/J Male (C57BL/6 x CBA)F1/J. 9 day differentiation of ES-TT2 cells in adherent monolayer culture (Gilbert) Shows smoothed wavelet over all phases ES-TT2 NP 9 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsem5sUDiffhsoxpWaveSignalRep2 Endoderm Ws 2 E0 ES-EM5Sox17huCD25 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEM002978 2978 Gilbert FSU-m GPL9156 2 U 129/Ola wgEncodeFsuRepliChipEsem5sUDiffhsoxpWaveSignalRep2 diffProtH_Sox17+ WaveSignal Embryonic day 0 (stem cell) ES cell line that bears the gfp and human IL2R alpha (also known as CD25) marker genes in the goosecoid (Gsc) and Sox17 loci, derived from EB5 Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Unknown The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Differentiation of ES-GscgfpSox17huCD25 towards endoderm cells after treatment with serum-free medium, SFO3, containing activin (10 ng/ml). After 6 days, cells were collected for Gsc+Sox17+ by fluorescence activated cell sorting (FACS). (Gilbert) Shows smoothed wavelet over all phases Endoderm Gsc/Sox17+ Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsem5sUDiffhsoxpWaveSignalRep1 Endoderm Ws 1 E0 ES-EM5Sox17huCD25 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEM002978 2978 Gilbert FSU-m GPL9156 1 U 129/Ola wgEncodeFsuRepliChipEsem5sUDiffhsoxpWaveSignalRep1 diffProtH_Sox17+ WaveSignal Embryonic day 0 (stem cell) ES cell line that bears the gfp and human IL2R alpha (also known as CD25) marker genes in the goosecoid (Gsc) and Sox17 loci, derived from EB5 Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Unknown The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Differentiation of ES-GscgfpSox17huCD25 towards endoderm cells after treatment with serum-free medium, SFO3, containing activin (10 ng/ml). After 6 days, cells were collected for Gsc+Sox17+ by fluorescence activated cell sorting (FACS). (Gilbert) Shows smoothed wavelet over all phases Endoderm Gsc/Sox17+ Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsem5sUDiffhsoxmWaveSignalRep2 Mesoderm Ws 2 E0 ES-EM5Sox17huCD25 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEM002977 2977 Gilbert FSU-m GPL9156 2 U 129/Ola wgEncodeFsuRepliChipEsem5sUDiffhsoxmWaveSignalRep2 diffProtH_Sox17- WaveSignal Embryonic day 0 (stem cell) ES cell line that bears the gfp and human IL2R alpha (also known as CD25) marker genes in the goosecoid (Gsc) and Sox17 loci, derived from EB5 Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Unknown The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Differentiation of ES-GscgfpSox17huCD25 towards mesoderm cells after treatment with serum-free medium, SFO3, containing activin (10 ng/ml). After 6 days, cells were collected for Gsc+Sox17- by fluorescence activated cell sorting (FACS). (Gilbert) Shows smoothed wavelet over all phases Mesoderm Gsc/Sox17- Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsem5sUDiffhsoxmWaveSignalRep1 Mesoderm Ws 1 E0 ES-EM5Sox17huCD25 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEM002977 2977 Gilbert FSU-m GPL9156 1 U 129/Ola wgEncodeFsuRepliChipEsem5sUDiffhsoxmWaveSignalRep1 diffProtH_Sox17- WaveSignal Embryonic day 0 (stem cell) ES cell line that bears the gfp and human IL2R alpha (also known as CD25) marker genes in the goosecoid (Gsc) and Sox17 loci, derived from EB5 Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Unknown The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Differentiation of ES-GscgfpSox17huCD25 towards mesoderm cells after treatment with serum-free medium, SFO3, containing activin (10 ng/ml). After 6 days, cells were collected for Gsc+Sox17- by fluorescence activated cell sorting (FACS). (Gilbert) Shows smoothed wavelet over all phases Mesoderm Gsc/Sox17- Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsd3MWaveSignalRep2 ES-D3 Ws 2 E0 ES-D3 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002968 2968 Gilbert FSU-m ES-D3_R2 GPL9156 2 M 129 wgEncodeFsuRepliChipEsd3MWaveSignalRep2 None WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from 129S2/SvPas Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Strain 129, has widely available embryonic stem cells Shows smoothed wavelet over all phases ES-D3 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsd3MWaveSignalRep1 ES-D3 Ws 1 E0 ES-D3 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002968 2968 Gilbert FSU-m ES-D3_R1 GPL9156 1 M 129 wgEncodeFsuRepliChipEsd3MWaveSignalRep1 None WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from 129S2/SvPas Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Strain 129, has widely available embryonic stem cells Shows smoothed wavelet over all phases ES-D3 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsd3MDiffg3dWaveSignalRep2 ES-D3 EPL Ws 2 E0 ES-D3 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEM002976 2976 Gilbert FSU-m GPL9156 2 M 129S2/SvPas wgEncodeFsuRepliChipEsd3MDiffg3dWaveSignalRep2 diffProtG_3d WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from 129S2/SvPas Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male The mice have white (or light)-bellied agouti. 3 day differentiation of ES-D3 cells with conditioned medium MEDII to form attached monolayer cells, early primitive ectoderm-like cells (EPL) (Gilbert) Shows smoothed wavelet over all phases ES-D3 EPL 3 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsd3MDiffg3dWaveSignalRep1 ES-D3 EPL Ws 1 E0 ES-D3 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2013-03-18 wgEncodeEM002976 2976 Gilbert FSU-m GPL9156 1 M 129S2/SvPas wgEncodeFsuRepliChipEsd3MDiffg3dWaveSignalRep1 diffProtG_3d WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from 129S2/SvPas Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male The mice have white (or light)-bellied agouti. 3 day differentiation of ES-D3 cells with conditioned medium MEDII to form attached monolayer cells, early primitive ectoderm-like cells (EPL) (Gilbert) Shows smoothed wavelet over all phases ES-D3 EPL 3 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsd3MDiffe9dWaveSignalRep2 ES-D3 NP Ws 2 E0 ES-D3 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002967 2967 Gilbert FSU-m NP-D3_R2 GPL9156 2 M 129 wgEncodeFsuRepliChipEsd3MDiffe9dWaveSignalRep2 diffProtE_9d WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from 129S2/SvPas Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Strain 129, has widely available embryonic stem cells 9 day differentiation of ES-D3 cells with conditioned medium MEDII to form neural precursor cells (Gilbert) Shows smoothed wavelet over all phases ES-D3 NP 9 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsd3MDiffe9dWaveSignalRep1 ES-D3 NP Ws 1 E0 ES-D3 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002967 2967 Gilbert FSU-m NP-D3_R1 GPL9156 1 M 129 wgEncodeFsuRepliChipEsd3MDiffe9dWaveSignalRep1 diffProtE_9d WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from 129S2/SvPas Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Strain 129, has widely available embryonic stem cells 9 day differentiation of ES-D3 cells with conditioned medium MEDII to form neural precursor cells (Gilbert) Shows smoothed wavelet over all phases ES-D3 NP 9 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsd3MDiffe6dWaveSignalRep2 ES-D3 EBM6 Ws 2 E0 ES-D3 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002966 2966 Gilbert FSU-m EBM6_R2 GPL9156 2 M 129 wgEncodeFsuRepliChipEsd3MDiffe6dWaveSignalRep2 diffProtE_6d WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from 129S2/SvPas Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Strain 129, has widely available embryonic stem cells 6 day differentiation of ES-D3 cells with conditioned medium MEDII to form neural precursor cells (Gilbert) Shows smoothed wavelet over all phases ES-D3 EBM 6 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsd3MDiffe6dWaveSignalRep1 ES-D3 EBM6 Ws 1 E0 ES-D3 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002966 2966 Gilbert FSU-m EBM6_R1 GPL9156 1 M 129 wgEncodeFsuRepliChipEsd3MDiffe6dWaveSignalRep1 diffProtE_6d WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from 129S2/SvPas Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Strain 129, has widely available embryonic stem cells 6 day differentiation of ES-D3 cells with conditioned medium MEDII to form neural precursor cells (Gilbert) Shows smoothed wavelet over all phases ES-D3 EBM 6 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsd3MDiffe3dWaveSignalRep2 ES-D3 EBM3 Ws 2 E0 ES-D3 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002965 2965 Gilbert FSU-m EBM3_R2 GPL9156 2 M 129 wgEncodeFsuRepliChipEsd3MDiffe3dWaveSignalRep2 diffProtE_3d WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from 129S2/SvPas Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Strain 129, has widely available embryonic stem cells 3 day differentiation of ES-D3 cells with conditioned medium MEDII to form neural precursor cells (Gilbert) Shows smoothed wavelet over all phases ES-D3 EBM 3 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEsd3MDiffe3dWaveSignalRep1 ES-D3 EBM3 Ws 1 E0 ES-D3 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002965 2965 Gilbert FSU-m EBM3_R1 GPL9156 1 M 129 wgEncodeFsuRepliChipEsd3MDiffe3dWaveSignalRep1 diffProtE_3d WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from 129S2/SvPas Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Strain 129, has widely available embryonic stem cells 3 day differentiation of ES-D3 cells with conditioned medium MEDII to form neural precursor cells (Gilbert) Shows smoothed wavelet over all phases ES-D3 EBM 3 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEs46cMWaveSignalRep1 ES-46C Ws 1 E0 ES-46C RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002964 2964 Gilbert FSU-m ES-46C_R1 GPL9156 1 M 129 wgEncodeFsuRepliChipEs46cMWaveSignalRep1 None WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from 129. Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Strain 129, has widely available embryonic stem cells Shows smoothed wavelet over all phases ES-46C Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEs46cMDifff6dWaveSignalRep1 ES-46C NP Ws 1 E0 ES-46C RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002963 2963 Gilbert FSU-m NP-46C_R1 GPL9156 1 M 129 wgEncodeFsuRepliChipEs46cMDifff6dWaveSignalRep1 diffProtF_6d WaveSignal Embryonic day 0 (stem cell) ES-cells isolated from 129. Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Strain 129, has widely available embryonic stem cells 6 day differentiation of ES-46C cells in adherent monolayer culture (Gilbert) Shows smoothed wavelet over all phases ES-46C NP 6 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEpisc7FWaveSignalRep2 EpiSC-7 Ws 2 E0 EpiSC-7 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002972 2972 Gilbert FSU-m EpiSC7_R2 GPL9156 2 F 129 wgEncodeFsuRepliChipEpisc7FWaveSignalRep2 None WaveSignal Embryonic day 0 (stem cell) epidermal stem cell Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Female Strain 129, has widely available embryonic stem cells Shows smoothed wavelet over all phases EpiSC-7 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEpisc7FWaveSignalRep1 EpiSC-7 Ws 1 E0 EpiSC-7 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002972 2972 Gilbert FSU-m EpiSC7_R1 GPL9156 1 F 129 wgEncodeFsuRepliChipEpisc7FWaveSignalRep1 None WaveSignal Embryonic day 0 (stem cell) epidermal stem cell Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Female Strain 129, has widely available embryonic stem cells Shows smoothed wavelet over all phases EpiSC-7 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEpisc5MWaveSignalRep2 EpiSC-5 Ws 2 E0 EpiSC-5 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002971 2971 Gilbert FSU-m EpiSC5_R2 GPL9156 2 M 129 wgEncodeFsuRepliChipEpisc5MWaveSignalRep2 None WaveSignal Embryonic day 0 (stem cell) epidermal stem cell Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Strain 129, has widely available embryonic stem cells Shows smoothed wavelet over all phases EpiSC-5 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipEpisc5MWaveSignalRep1 EpiSC-5 Ws 1 E0 EpiSC-5 RepliChip ENCODE Jul 2012 Freeze 2012-06-18 2012-03-31 2012-12-30 wgEncodeEM002971 2971 Gilbert FSU-m EpiSC5_R1 GPL9156 1 M 129 wgEncodeFsuRepliChipEpisc5MWaveSignalRep1 None WaveSignal Embryonic day 0 (stem cell) epidermal stem cell Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University FSU NimbleGen Mouse 385K Whole Genome Tiling Male Strain 129, has widely available embryonic stem cells Shows smoothed wavelet over all phases EpiSC-5 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipCh12FWaveSignalRep2 CH12 Ws 2 immortalized CH12 RepliChip ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002962 2962 Gilbert FSU-m CH12_R2 GPL10989 2 F B10.H-2aH-4bp/Wts wgEncodeFsuRepliChipCh12FWaveSignalRep2 None WaveSignal Immortal cells B-cell lymphoma (GM12878 analog) Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University NimbleGen Mouse CGH 3x720K Whole-Genome Tiling (FSU) Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Shows smoothed wavelet over all phases CH12 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU Expression and Regulation 
wgEncodeFsuRepliChipCh12FWaveSignalRep1 CH12 Ws 1 immortalized CH12 RepliChip ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002962 2962 Gilbert FSU-m CH12_R1 GPL10989 1 F B10.H-2aH-4bp/Wts wgEncodeFsuRepliChipCh12FWaveSignalRep1 None WaveSignal Immortal cells B-cell lymphoma (GM12878 analog) Assessment of DNA Replication Timing Gilbert Gilber - The Florida State University NimbleGen Mouse CGH 3x720K Whole-Genome Tiling (FSU) Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Shows smoothed wavelet over all phases CH12 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU Expression and Regulation 
gap Gap Gap Locations Mapping and Sequencing Description This track depicts gaps in the assembly. These gaps - with the exception of intractable centromere gaps - will be closed during the finishing process. Gaps are represented as black boxes in this track. If the relative order and orientation of the contigs on either side of the gap is known, it is a bridged gap and a white line is drawn through the black box representing the gap. This assembly contains the following principal types of gaps: Fragment - gaps between the contigs of a draft clone. (In this context, a contig is a set of overlapping sequence reads.) Contig - gaps between map contigs. Centromere - gaps from centromeres (3,000,000 Ns) or other large blocks of heterochromatin (size varies). 
gc5Base GC Percent GC Percent in 5-Base Windows Mapping and Sequencing Description The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas. This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the &quot;Graph configuration help&quot; link for an explanation of the configuration options. Credits The data and presentation of this graph were prepared by Hiram Clawson. 
igtc Gene Trap International Gene Trap Consortium Sequence Tag Alignments Genes and Gene Predictions Description This track shows alignments of International Gene Trap Consortium sequence tags to the mouse genome. Items are labeled by cell line and colored by source: BG: BayGenomics (USA) CMHD: Centre for Modeling Human Disease (Toronto, Canada) EGTC: Exchangeable Gene Trap Clones (Kumamoto University, Japan) ESDB: Embryonic Stem Cell Database (University of Manitoba, Canada) FHCRC: Soriano Lab Gene Trap Database (originally at Fred Hutchinson Cancer Research Center, Seattle, USA; now at Mount Sinai School of Medicine, Manhattan, NY) GGTC: German Gene Trap Consortium (Germany) SIGTR: Sanger Institute Gene Trap Resource (Cambridge, UK) TIGEM: TIGEM-IRBM Gene Trap (Naples, Italy) TIGM: Texas Institute for Genomic Medicine (Houston, Texas) Methods The IGTC pipeline uses BLAT to align sequence tags from dbGSS to the mouse genome and BLAST to match sequence tags to genes. The pipeline filters and reconciles the two sets of alignments to associate cell lines with trapped genes. Credits Thanks to the International Gene Trap Consortium for providing this track. 
geneid Geneid Genes Geneid Gene Predictions Genes and Gene Predictions Description This track shows gene predictions from the geneid program developed by Roderic Guig&oacute;'s Computational Biology of RNA Processing group which is part of the Centre de Regulaci&oacute; Gen&ograve;mica (CRG) in Barcelona, Catalunya, Spain. Methods Geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the the log-likelihood ratio of a Markov Model for coding DNA. Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. Credits Thanks to Computational Biology of RNA Processing for providing these data. References Blanco E, Parra G, Guig&#243; R. Using geneid to identify genes. Curr Protoc Bioinformatics. 2007 Jun;Chapter 4:Unit 4.3. PMID: 18428791 Parra G, Blanco E, Guig&#243; R. GeneID in Drosophila. Genome Res. 2000 Apr;10(4):511-5. PMID: 10779490; PMC: PMC310871 
genscan Genscan Genes Genscan Gene Predictions Genes and Gene Predictions Description This track shows predictions from the Genscan program written by Chris Burge. The predictions are based on transcriptional, translational and donor/acceptor splicing signals as well as the length and compositional distributions of exons, introns and intergenic regions. For more information on the different gene tracks, see our Genes FAQ. Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. The track description page offers the following filter and configuration options: Color track by codons: Select the genomic codons option to color and label each codon in a zoomed-in display to facilitate validation and comparison of gene predictions. Go to the Coloring Gene Predictions and Annotations by Codon page for more information about this feature. Methods For a description of the Genscan program and the model that underlies it, refer to Burge and Karlin (1997) in the References section below. The splice site models used are described in more detail in Burge (1998) below. Credits Thanks to Chris Burge for providing the Genscan program. References Burge C. Modeling Dependencies in Pre-mRNA Splicing Signals. In: Salzberg S, Searls D, Kasif S, editors. Computational Methods in Molecular Biology. Amsterdam: Elsevier Science; 1998. p. 127-163. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 1997 Apr 25;268(1):78-94. PMID: 9149143 
gnfAtlas2 GNF Atlas 2 GNF Expression Atlas 2 Expression and Regulation Description This track shows expression data from the GNF Gene Expression Atlas 2. This contains two replicates each of 61 mouse tissues run over Affymetrix microarrays. By default, averages of related tissues are shown. Display all tissues by selecting &quot;All Arrays&quot; from the &quot;Combine arrays&quot; menu on the track settings page. As is standard with microarray data red indicates overexpression in the tissue, and green indicates underexpression. You may want to view gene expression with the Gene Sorter as well as the Genome Browser. Credits Thanks to the Genomics Institute of the Novartis Research Foundation (GNF) for the data underlying this track. References Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7. PMID: 15075390; PMC: PMC395923 
affyGnfU74A GNF U74A GNF Expression Atlas on Mouse Affymetrix U74A Chip Expression and Regulation Description This track shows expression data from GNF (The Genomics Institute of the Novartis Research Foundation) using the Affymetrix U74A chip. Methods For detailed information about the experiments, see Su et al. (2002) in the References section below. Alignments displayed on the track correspond to the consensus sequences used by Affymetrix to choose probes. In dense mode, the track color denotes the average signal over all experiments on a log base 2 scale. Lighter colors correspond to lower signals; darker colors correspond to higher signals. In full mode, the color of each item represents the log base 2 ratio of the signal of that particular experiment to the median signal of all experiments for that probe. More information about individual probes and probe sets is available at Affymetrix's NetAffx website. Credits Thanks to GNF for providing these data. References Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4465-70. PMID: 11904358; PMC: PMC123671 
affyGnfU74B GNF U74B GNF Expression Atlas on Mouse Affymetrix U74B Chip Expression and Regulation Description This track shows expression data from GNF (The Genomics Institute of the Novartis Research Foundation) using the Affymetrix U74B chip. Methods For detailed information about the experiments, see Su et al. (2002) in the References section below. Alignments displayed on the track correspond to the consensus sequences used by Affymetrix to choose probes. In dense mode, the track color denotes the average signal over all experiments on a log base 2 scale. Lighter colors correspond to lower signals; darker colors correspond to higher signals. In full mode, the color of each item represents the log base 2 ratio of the signal of that particular experiment to the median signal of all experiments for that probe. More information about individual probes and probe sets is available at Affymetrix's NetAffx website. Credits Thanks to GNF for providing these data. References Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4465-70. PMID: 11904358; PMC: PMC123671 
affyGnfU74C GNF U74C GNF Expression Atlas on Mouse Affymetrix U74C Chip Expression and Regulation Description This track shows expression data from GNF (The Genomics Institute of the Novartis Research Foundation) using the Affymetrix U74C chip. Methods For detailed information about the experiments, see Su et al. (2002) in the References section below. Alignments displayed on the track correspond to the consensus sequences used by Affymetrix to choose probes. In dense mode, the track color denotes the average signal over all experiments on a log base 2 scale. Lighter colors correspond to lower signals and darker colors correspond to higher signals. In full mode, the color of each item represents the log base 2 ratio of the signal of that particular experiment to the median signal of all experiments for that probe. More information about individual probes and probe sets is available at Affymetrix's NetAffx website. Credits Thanks to GNF for providing these data. References Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4465-70. PMID: 11904358; PMC: PMC123671 
grcIncidentDb GRC Incident GRC Incident Database Mapping and Sequencing Description This track shows locations in the mouse assembly where assembly problems have been noted or resolved, as reported by the Genome Reference Consortium (GRC). If you would like to report an assembly problem, please use the GRC issue reporting system. Methods Data for this track are extracted from the GRC incident database from the specific species *_issues.gff3 file. The track is synchronized once daily to incorporate new updates. Credits The data and presentation of this track were prepared by Hiram Clawson. 
ikmc IKMC Genes International Knockout Mouse Consortium Genes Genes and Gene Predictions Description This track shows genes targeted by International Knockout Mouse Consortium (IKMC), a collaboration to generate a public resource of mouse embryonic stem (ES) cells containing a null mutation in every gene in the mouse genome. Gene targets are color-coded by status: Green: Reagent(s) Available Yellow: In Progress Blue: Not Started/On Hold Black: Withdrawn/Problematic The KnockOut Mouse Project Data Coordination Center (KOMP DCC) is the central database resource for coordinating mouse gene targeting within IKMC and provides web-based query and display tools for IKMC data. In addition, the KOMP DCC website provides a tool for the scientific community to nominate genes of interest to be knocked out by the KOMP initiative. IKMC members include KnockOut Mouse Project (KOMP), a trans-NIH initiative (USA) European Conditional Mouse Mutagenesis Program (EUCOMM), funded by the European Union Framework 6 programme (EU) North American Conditional Mouse Mutagenesis Project (NorCOMM), a Genome Prairie Project (Canada) Texas A&amp;M Institute for Genomic Medicine (TIGM) (USA) KOMP includes two production centers: CSD, a collaborative team at the Children's Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine, and a team at the VelociGene division of Regeneron Pharmaceuticals, Inc. EUCOMM includes 9 participating institutions. NorCOMM includes several participating institutions. Items displayed as a solid box represent the gene regions targeted by the Regeneron gene knockout strategy. In most cases Regeneron alleles will be complete null alleles that delete the entire protein coding sequence of the target gene. Items displayed as lines connecting short boxes represent the targeting vector construct strategy used by EuCOMM, NorCOMM, and CSD. This strategy relies on the identification of a &quot;critical&quot; exon common to all transcript variants that, when deleted, creates a frame-shift mutation. The short boxes in the middle of an item show the vector features that surround the critical exon. Methods Using complementary targeting strategies, the IKMC centers design and create targeting vectors, mutant ES cell lines and, to some extent, mutant mice, embryos or sperm. Materials are distributed to the research community. The KOMP Repository archives, maintains, and distributes IKMC products. Researchers can order products and get product information from the Repository. Researchers can also express interest in products that are still in the pipeline. They will then receive email notification as soon as KOMP generated products are available for distribution. The process for ordering EUCOMM materials can be found here. The process for ordering TIGM materials can be found here. Information on NorCOMM products and services can be found here. Credits Thanks to the International Knockout Mouse Consortium, and Carol Bult in particular, for providing these data. References Austin CP, Battey JF, Bradley A, Bucan M, Capecchi M, Collins FS, Dove WF, Duyk G, Dymecki S, Eppig JT et al. The knockout mouse project. Nat Genet. 2004 Sep;36(9):921-4. PMID: 15340423; PMC: PMC2716027 Collins FS, Finnell RH, Rossant J, Wurst W. A new partner for the international knockout mouse consortium. Cell. 2007 Apr 20;129(2):235. PMID: 17448981 International Mouse Knockout Consortium, Collins FS, Rossant J, Wurst W. A mouse for all reasons. Cell. 2007 Jan 12;128(1):9-13. PMID: 17218247 
wgEncodeLicrHistone LICR Histone GSE31039 Histone Mods by ChIP-seq from ENCODE/LICR Expression and Regulation Description This track shows a comprehensive survey of cis-regulatory elements in the mouse genome by using ChIP-seq &#40;Robertson et al., 2007&#41; to identify transcription factor binding sites and chromatin modification profiles in various mouse &#40;C57BL/6, 129/Ola&#41; tissues, primary cells, and cell lines. The Ren lab examined RNA polymerase II &#40;PolII&#41;, co-activator protein p300, the insulator protein CTCF, and the following chromatin modification marks: H3K4me3 and H3K4me1, H3K27ac, H3K36me3, H3K9me3, and H3K27me3 due to their demonstrated utilities in identifying promoters, enhancers, insulator elements, actively transcribed gene bodies, and silent chromatin regions &#40;Barski et al., 2007; Bernstein et al., 2006; Blow et al., 2010; Creyghton et al., 2010; Francis et al., 2004; Hawkins et al., 2011; Heintzman et al., 2009; Kim et al. , 2007; Kim et al., 2005; Krogan et al., 2003; Li et al., 2002; Peters et al., 2001; Rada-Iglesias et al. , 2011; Schotta et al., 2002; Visel et al., 2009&#41;. Enrichment of PolII signals is a strong indicator of an active promoter and the presence of p300 outside of promoter regions has been used as a mark for enhancers. CTCF binding sites are considered as a mark for potential insulator elements. H3K4me3 is an active mark for promoters and H3K27ac is an active mark for both promoters and enhancers. In the absence of H3K4me3, H3K4me1 serves as an active mark for enhancers. H3K36me3 is normally found in actively transcribed gene bodies whereas both H3K9me3 and H3K27me3 are common repressive marks for transcriptionally silent chromatin regions. For each transcription factor or chromatin mark in each tissue, ChIP-seq was carried out with at least two biological replicates. Each experiment produced 20-30 million uniquely-mapped monoclonal tags. 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. This track contains the following views: Peaks Regions of signal enrichment based on processed data (normalized data from pooled replicates). Intensity is represented in grayscale; darker shading shows higher intensity (a solid vertical line in the peak region represents the point with the highest signal). 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. Additional views are available on the Downloads page. Methods Cells were grown according to the approved ENCODE cell culture protocols. Enrichment and Library Preparation Chromatin immunoprecipitation was performed according to the Ren Lab ChIP Protocol. Library construction was performed according to the Ren Lab Library Protocol. Sequencing and Analysis Samples were sequenced on Illumina Genome Analyzer II, Genome Analyzer IIx and HiSeq 2000 platforms for 36 cycles. Image analysis, base calling and alignment to the mouse genome version NCBI37/mm9 were performed using Illumina&#39;s RTA and Genome Analyzer Pipeline software. Alignment to the mouse genome was performed using ELAND or Bowtie (Langmead et al., 2009) with a seed length of 25 and allowing up to two mismatches. Only the sequences that mapped to one location were used for further analysis. Of those sequences, clonal reads, defined as having the same start position on the same strand, were discarded. BED and wig files were created using custom perl scripts. Release Notes This is Release 3 (Aug 2012). It contains a total of 130 Chip-seq experiments on histone modifications with the addition of 31 new experiments. Credits These data were generated and analyzed in Bing Ren&#39;s laboratory at the Ludwig Institute for Cancer Research (LICR). Contact: Yin Shen References Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell. 2007 May 18;129(4):823-37. 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. Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet. 2010 Sep;42(9):806-10. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6. Francis NJ, Kingston RE, Woodcock CL. Chromatin compaction by a polycomb group protein complex. Science. 2004 Nov 26;306(5701):1574-7. Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z et al. Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Res. 2011 Oct;21(10):1393-409. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 2009 May 7;459(7243):108-12. Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell. 2007 Mar 23;128(6):1231-45. Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM et al. Direct isolation and identification of promoters in the human genome. Genome Res. 2005 Jun;15(6):830-9. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C et al. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol. 2003 Jun;23(12):4207-18. 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 J, Moazed D, Gygi SP. Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. J Biol Chem. 2002 Dec 20;277(51):49383-8. Peters AH, O'Carroll D, Scherthan H, Mechtler K, Sauer S, Sch&#246;fer C, Weipoltshammer K, Pagani M, Lachner M, Kohlmaier A et al. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell. 2001 Nov 2;107(3):323-37. Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 2011 Feb 10;470(7333):279-83. 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. Schotta G, Ebert A, Krauss V, Fischer A, Hoffmann J, Rea S, Jenuwein T, Dorn R, Reuter G. Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing. EMBO J. 2002 Mar 1;21(5):1121-31. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009 Feb 12;457(7231):854-8. 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. 
wgEncodeLicrHistoneViewSignal Signal Histone Mods by ChIP-seq from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainInputUE14halfC57bl6StdSig Brain Input E14.5 Input WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-23 wgEncodeEM002494 2494 GSM1000098 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input U Custom Scripts C57BL/6 wgEncodeLicrHistoneWbrainInputUE14halfC57bl6StdSig Signal Embryonic day 14.5 Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain E14.5 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainH3k36me3ME14halfC57bl6StdSig Brain H3K36m3 E14.5 H3K36me3 WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002718 2718 GSM1000072 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneWbrainH3k36me3ME14halfC57bl6StdSig Signal Embryonic day 14.5 Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain E14.5 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainH3k27me3ME14halfC57bl6StdSig Brain H3K27m3 E14.5 H3K27me3 WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002725 2725 GSM1000143 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneWbrainH3k27me3ME14halfC57bl6StdSig Signal Embryonic day 14.5 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. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain E14.5 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainH3k27acUE14halfC57bl6StdSig Brain H3K27a E14.5 H3K27ac WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-23 wgEncodeEM002491 2491 GSM1000094 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrHistoneWbrainH3k27acUE14halfC57bl6StdSig Signal Embryonic day 14.5 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. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain E14.5 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainH3k09me3ME14halfC57bl6StdSig Brain H3K9m3 E14.5 H3K9me3 WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002726 2726 GSM1000106 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneWbrainH3k09me3ME14halfC57bl6StdSig Signal Embryonic day 14.5 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. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain E14.5 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainH3k04me3UE14halfC57bl6StdSig Brain H3K4m3 E14.5 H3K4me3 WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-23 wgEncodeEM002493 2493 GSM1000095 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrHistoneWbrainH3k04me3UE14halfC57bl6StdSig Signal Embryonic day 14.5 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain E14.5 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainH3k04me1UE14halfC57bl6StdSig Brain H3K4m1 E14.5 H3K4me1 WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-23 wgEncodeEM002492 2492 GSM1000096 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrHistoneWbrainH3k04me1UE14halfC57bl6StdSig Signal Embryonic day 14.5 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain E14.5 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneThymusInputMAdult8wksC57bl6StdSig Thymus Input adult-8wks Input Thymus std ChipSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002477 2477 GSM1000204 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneThymusInputMAdult8wksC57bl6StdSig Signal Adult 8 weeks Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Thymus 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneThymusH3k36me3MAdult8wksC57bl6StdSig Thymus H3K36m3 adult-8wks H3K36me3 Thymus std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEM002717 2717 GSM1000068 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneThymusH3k36me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Thymus 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneThymusH3k27me3MAdlt8wC57bl6StdSig Thymus H3K27m3 adult-8wks H3K27me3 Thymus std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002724 2724 GSM1000144 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneThymusH3k27me3MAdlt8wC57bl6StdSig Signal Adult 8 weeks 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. Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Thymus 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneThymusH3k27acMAdult8wksC57bl6StdSig Thymus H3K27a adult-8wks H3K27ac Thymus std ChipSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002474 2474 GSM1000103 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneThymusH3k27acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Thymus 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneThymusH3k04me3MAdult8wksC57bl6StdSig Thymus H3K4m3 adult-8wks H3K4me3 Thymus std ChipSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002476 2476 GSM1000101 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneThymusH3k04me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Thymus 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneThymusH3k04me1MAdult8wksC57bl6StdSig Thymus H3K4m1 adult-8wks H3K4me1 Thymus std ChipSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002475 2475 GSM1000102 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneThymusH3k04me1MAdult8wksC57bl6StdSig Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Thymus 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneTestisInputMAdult8wksC57bl6StdSig Testis Input adult-8wks Input Testis std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002490 2490 GSM1000203 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneTestisInputMAdult8wksC57bl6StdSig Signal Adult 8 weeks Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Testis 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneTestisH3k36me3MAdult8wksC57bl6StdSig Testis H3K36m3 adult-8wks H3K36me3 Testis std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002716 2716 GSM1000067 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneTestisH3k36me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Testis 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneTestisH3k27me3MAdlt8wC57bl6StdSig Testis H3K27m3 adult-8wks H3K27me3 Testis std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002723 2723 GSM1000145 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneTestisH3k27me3MAdlt8wC57bl6StdSig Signal Adult 8 weeks 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. Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Testis 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneTestisH3k27acMAdult8wksC57bl6StdSig Testis H3K27a adult-8wks H3K27ac Testis std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002487 2487 GSM1000081 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneTestisH3k27acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Testis 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneTestisH3k04me3MAdult8wksC57bl6StdSig Testis H3K4m3 adult-8wks H3K4me3 Testis std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002489 2489 GSM1000079 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneTestisH3k04me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Testis 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneTestisH3k04me1MAdult8wksC57bl6StdSig Testis H3K4m1 adult-8wks H3K4me1 Testis std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002488 2488 GSM1000078 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneTestisH3k04me1MAdult8wksC57bl6StdSig Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Testis 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSpleenInputMAdult8wksC57bl6StdSig Spleen Input adult-8wks Input Spleen std ChipSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001459 1459 GSM769037 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneSpleenInputMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Spleen 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSpleenH3k36me3MAdult8wksC57bl6StdSig Spleen H3K36m3 adult-8wks H3K36me3 Spleen std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEM002715 2715 GSM1000070 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneSpleenH3k36me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Spleen 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSpleenH3k27me3MAdlt8wC57bl6StdSig Spleen H3K27m3 adult-8wks H3K27me3 Spleen std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002722 2722 GSM1000146 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneSpleenH3k27me3MAdlt8wC57bl6StdSig Signal Adult 8 weeks 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. Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Spleen 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSpleenH3k27acMAdult8wksC57bl6StdSig Spleen H3K27a adult-8wks H3K27ac Spleen std ChipSeq ENCODE Mar 2012 Freeze 2011-12-24 2012-09-23 wgEncodeEM002502 2502 GSM1000138 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneSpleenH3k27acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Spleen 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSpleenH3k4me3MAdult8wksC57bl6StdSig Spleen H3K4m3 adult-8wks H3K4me3 Spleen std ChipSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-01 wgEncodeEM001458 1458 GSM769036 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneSpleenH3k4me3MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Spleen 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSpleenH3k4me1MAdult8wksC57bl6StdSig Spleen H3K4m1 adult-8wks H3K4me1 Spleen std ChipSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-01 wgEncodeEM001457 1457 GSM769031 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneSpleenH3k4me1MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Spleen 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSmintInputMAdult8wksC57bl6StdSig SmInt Input adult-8wks Input SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002486 2486 GSM1000080 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneSmintInputMAdult8wksC57bl6StdSig Signal Adult 8 weeks Small Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Small Intestine 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSmintH3k36me3MAdult8wksC57bl6StdSig SmInt H3K36m3 adult-8wks H3K36me3 SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002714 2714 GSM1000069 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneSmintH3k36me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks 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 Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Small Intestine 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSmintH3k27me3MAdult8wksC57bl6StdSig SmInt H3K27m3 adult-8wks H3K27me3 SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002713 2713 GSM1000064 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneSmintH3k27me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks 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 Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Small Intestine 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSmintH3k27acMAdult8wksC57bl6StdSig SmInt H3K27a adult-8wks H3K27ac SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002483 2483 GSM1000084 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneSmintH3k27acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Small Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Small Intestine 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSmintH3k04me3MAdult8wksC57bl6StdSig SmInt H3K4m3 adult-8wks H3K4me3 SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002485 2485 GSM1000083 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneSmintH3k04me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Small Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Small Intestine 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSmintH3k04me1MAdult8wksC57bl6StdSig SmInt H3K4m1 adult-8wks H3K4me1 SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002484 2484 GSM1000082 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneSmintH3k04me1MAdult8wksC57bl6StdSig Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Small Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Small Intestine 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistonePlacInputFAdult8wksC57bl6StdSig Placenta Input adult-8wks Input Placenta std ChipSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002510 2510 GSM1000207 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input F Custom Scripts C57BL/6 wgEncodeLicrHistonePlacInputFAdult8wksC57bl6StdSig Signal Adult 8 weeks Placenta Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal Placenta 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistonePlacH3k27acFAdult8wksC57bl6StdSig Placenta H3K27a adult-8wks H3K27ac Placenta std ChipSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002507 2507 GSM1000134 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistonePlacH3k27acFAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Placenta Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal Placenta 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistonePlacH3k04me3FAdult8wksC57bl6StdSig Placenta H3K4m3 adult-8wks H3K4me3 Placenta std ChipSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002509 2509 GSM1000132 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistonePlacH3k04me3FAdult8wksC57bl6StdSig Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Placenta Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal Placenta 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistonePlacH3k04me1FAdult8wksC57bl6StdSig Placenta H3K4m1 adult-8wks H3K4me1 Placenta std ChipSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-05 wgEncodeEM002508 2508 GSM1000133 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistonePlacH3k04me1FAdult8wksC57bl6StdSig Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Placenta Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal Placenta 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneOlfactInputMAdult8wksC57bl6StdSig Olfact Input adult-8wks Input OlfactBulb std ChipSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002473 2473 GSM1000205 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneOlfactInputMAdult8wksC57bl6StdSig Signal Adult 8 weeks Olfactory Bulb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Olfactory Bulb 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneOlfactH3k27acMAdult8wksC57bl6StdSig Olfact H3K27a adult-8wks H3K27ac OlfactBulb std ChipSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002471 2471 GSM1000105 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneOlfactH3k27acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Olfactory Bulb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Olfactory Bulb 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneOlfactH3k04me3MAdult8wksC57bl6StdSig Olfact H3K4m3 adult-8wks H3K4me3 OlfactBulb std ChipSeq ENCODE Mar 2012 Freeze 2012-01-07 2012-10-06 wgEncodeEM002511 2511 GSM1000128 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneOlfactH3k04me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Olfactory Bulb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Olfactory Bulb 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneOlfactH3k04me1MAdult8wksC57bl6StdSig Olfact H3K4m1 adult-8wks H3K4me1 OlfactBulb std ChipSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002472 2472 GSM1000104 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneOlfactH3k04me1MAdult8wksC57bl6StdSig Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Olfactory Bulb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Olfactory Bulb 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelInputMImmortalC57bl6StdSig MEL Input immortalized Input MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM002652 2652 GSM1000200 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 input M Custom Scripts Unknown wgEncodeLicrHistoneMelInputMImmortalC57bl6StdSig Signal Immortal cells Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Signal MEL Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k79me2MImmortalC57bl6StdSig MEL H3K79m2 immortalized H3K79me2 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002647 2647 GSM1000156 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts Unknown wgEncodeLicrHistoneMelH3k79me2MImmortalC57bl6StdSig Signal Immortal cells H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Signal MEL H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k36me3MImmortalC57bl6StdSig MEL H3K36m3 immortalized H3K36me3 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002646 2646 GSM1000155 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts Unknown wgEncodeLicrHistoneMelH3k36me3MImmortalC57bl6StdSig Signal Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Signal MEL H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k27me3MImmortalC57bl6StdSig MEL H3K27m3 immortalized H3K27me3 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002645 2645 GSM1000154 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts Unknown wgEncodeLicrHistoneMelH3k27me3MImmortalC57bl6StdSig Signal Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Signal MEL H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k27acMImmortalC57bl6StdSig MEL H3K27a immortalized H3K27ac MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-28 wgEncodeEM002649 2649 GSM1000142 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts Unknown wgEncodeLicrHistoneMelH3k27acMImmortalC57bl6StdSig Signal Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Signal MEL H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k09acMImmortalC57bl6StdSig MEL H3K9a immortalized H3K9ac MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002648 2648 GSM1000141 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts Unknown wgEncodeLicrHistoneMelH3k09acMImmortalC57bl6StdSig Signal Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Signal MEL H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k04me3MImmortalC57bl6StdSig MEL H3K4m3 immortalized H3K4me3 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-28 wgEncodeEM002651 2651 GSM1000087 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts Unknown wgEncodeLicrHistoneMelH3k04me3MImmortalC57bl6StdSig Signal Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Signal MEL H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k04me1MImmortalC57bl6StdSig MEL H3K4m1 immortalized H3K4me1 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-28 wgEncodeEM002650 2650 GSM1000073 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts Unknown wgEncodeLicrHistoneMelH3k04me1MImmortalC57bl6StdSig Signal Immortal cells Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Signal MEL H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMefInputMAdult8wksC57bl6StdSig MEF Input adult-8wks Input MEF std ChipSeq ENCODE Mar 2012 Freeze 2011-04-29 2012-01-28 wgEncodeEM001456 1456 GSM769030 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneMefInputMAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks Mouse Embryonic Fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal MEF 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMefH3k27acMAdult8wksC57bl6StdSig MEF H3K27a adult-8wks H3K27ac MEF std ChipSeq ENCODE Mar 2012 Freeze 2011-12-24 2012-09-23 wgEncodeEM002501 2501 GSM1000139 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneMefH3k27acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Mouse Embryonic Fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal MEF 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMefH3k4me3MAdult8wksC57bl6StdSig MEF H3K4m3 adult-8wks H3K4me3 MEF std ChipSeq ENCODE Mar 2012 Freeze 2011-04-29 2012-01-28 wgEncodeEM001455 1455 GSM769029 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneMefH3k4me3MAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Mouse Embryonic Fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal MEF 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMefH3k4me1MAdult8wksC57bl6StdSig MEF H3K4m1 adult-8wks H3K4me1 MEF std ChipSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEM001454 1454 GSM769028 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneMefH3k4me1MAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Mouse Embryonic Fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal MEF 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLungInputMAdult8wksC57bl6StdSig Lung Input adult-8wks Input Lung std ChipSeq ENCODE Mar 2012 Freeze 2011-04-27 2012-01-26 wgEncodeEM001453 1453 GSM769035 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneLungInputMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Lung Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Lung 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLungH3k4me3MAdult8wksC57bl6StdSig Lung H3K4m3 adult-8wks H3K4me3 Lung std ChipSeq ENCODE Mar 2012 Freeze 2011-04-15 2012-01-14 wgEncodeEM001446 1446 GSM769012 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneLungH3k4me3MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Lung Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Lung 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLungH3k4me1MAdult8wksC57bl6StdSig Lung H3K4m1 adult-8wks H3K4me1 Lung std ChipSeq ENCODE Mar 2012 Freeze 2011-04-15 2012-01-14 wgEncodeEM001445 1445 GSM769013 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneLungH3k4me1MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Lung Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Lung 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverInputUE14halfC57bl6StdSig Liver 14.5 Input E14.5 Input Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-13 wgEncodeEM002570 2570 GSM1000112 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input U Custom Scripts C57BL/6 wgEncodeLicrHistoneLiverInputUE14halfC57bl6StdSig Signal Embryonic day 14.5 Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Liver E14.5 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverInputMAdult8wksC57bl6StdSig Liver 8w Input adult-8wks Input Liver std ChipSeq ENCODE Mar 2012 Freeze 2011-04-27 2012-01-26 wgEncodeEM001452 1452 GSM769034 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneLiverInputMAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Liver 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k79me2MAdult8wksC57bl6StdSig Liver 8w H3K79m2 adult-8wks H3K79me2 Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002643 2643 GSM1000152 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneLiverH3k79me2MAdult8wksC57bl6StdSig Signal Adult 8 weeks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Liver 8w H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k36me3MAdult8wksC57bl6StdSig Liver 8w H3K36m3 adult-8wks H3K36me3 Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002642 2642 GSM1000151 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneLiverH3k36me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Liver 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k27me3MAdult8wksC57bl6StdSig Liver 8w H3K27m3 adult-8wks H3K27me3 Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002641 2641 GSM1000150 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneLiverH3k27me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Liver 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k27acUE14halfC57bl6StdSig Liver 14.5 H3K27a E14.5 H3K27ac Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002571 2571 GSM1000113 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrHistoneLiverH3k27acUE14halfC57bl6StdSig Signal Embryonic day 14.5 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. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Liver E14.5 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k27acMAdult8wksC57bl6StdSig Liver 8w H3K27a adult-8wks H3K27ac Liver std ChipSeq ENCODE Mar 2012 Freeze 2011-12-24 2012-09-23 wgEncodeEM002500 2500 GSM1000140 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneLiverH3k27acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Liver 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k09acMAdult8wksC57bl6StdSig Liver 8w H3K9a adult-8wks H3K9ac Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002644 2644 GSM1000153 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneLiverH3k09acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Liver 8w H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k04me3UE14halfC57bl6StdSig Liver 14.5 H3K4m3 E14.5 H3K4me3 Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002572 2572 GSM1000110 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrHistoneLiverH3k04me3UE14halfC57bl6StdSig Signal Embryonic day 14.5 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Liver E14.5 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k4me3MAdult8wksC57bl6StdSig Liver 8w H3K4m3 adult-8wks H3K4me3 Liver std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2012-01-12 wgEncodeEM001444 1444 GSM769014 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneLiverH3k4me3MAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Liver 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k04me1UE14halfC57bl6StdSig Liver 14.5 H3K4m1 E14.5 H3K4me1 Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002573 2573 GSM1000111 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrHistoneLiverH3k04me1UE14halfC57bl6StdSig Signal Embryonic day 14.5 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Liver E14.5 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k4me1MAdult8wksC57bl6StdSig Liver 8w H3K4m1 adult-8wks H3K4me1 Liver std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2012-01-12 wgEncodeEM001443 1443 GSM769015 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneLiverH3k4me1MAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Liver 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLimbInputUE14halfC57bl6StdSig Limb Input E14.5 Input Limb std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-23 wgEncodeEM002482 2482 GSM1000202 Ren LICR-m Pooled & filtered Illumina_GA2 input U Custom Scripts C57BL/6 wgEncodeLicrHistoneLimbInputUE14halfC57bl6StdSig Signal Embryonic day 14.5 Limb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Limb E14.5 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLimbH3k27acUE14halfC57bl6StdSig Limb H3K27a E14.5 H3K27ac Limb std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-23 wgEncodeEM002479 2479 GSM1000107 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrHistoneLimbH3k27acUE14halfC57bl6StdSig Signal Embryonic day 14.5 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. Limb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Limb E14.5 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLimbH3k04me3UE14halfC57bl6StdSig Limb H3K4m3 E14.5 H3K4me3 Limb std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-23 wgEncodeEM002481 2481 GSM1000086 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrHistoneLimbH3k04me3UE14halfC57bl6StdSig Signal Embryonic day 14.5 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Limb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Limb E14.5 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLimbH3k04me1UE14halfC57bl6StdSig Limb H3K4m1 E14.5 H3K4me1 Limb std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-23 wgEncodeEM002480 2480 GSM1000085 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrHistoneLimbH3k04me1UE14halfC57bl6StdSig Signal Embryonic day 14.5 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Limb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Limb E14.5 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneKidneyInputMAdult8wksC57bl6StdSig Kidney Input adult-8wks Input Kidney std ChipSeq ENCODE Mar 2012 Freeze 2011-04-27 2012-01-26 wgEncodeEM001451 1451 GSM769033 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneKidneyInputMAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Kidney 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneKidneyH3k36me3MAdult8wksC57bl6StdSig Kidney H3K36m3 adult-8wks H3K36me3 Kidney std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002712 2712 GSM1000063 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneKidneyH3k36me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Kidney 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneKidneyH3k27me3MAdult8wksC57bl6StdSig Kidney H3K27m3 adult-8wks H3K27me3 Kidney std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002711 2711 GSM1000077 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneKidneyH3k27me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Kidney 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneKidneyH3k27acMAdult8wksC57bl6StdSig Kidney H3K27a adult-8wks H3K27ac Kidney std ChipSeq ENCODE Mar 2012 Freeze 2011-12-24 2012-09-23 wgEncodeEM002499 2499 GSM1000092 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneKidneyH3k27acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Kidney 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneKidneyH3k4me3MAdult8wksC57bl6StdSig Kidney H3K4m3 adult-8wks H3K4me3 Kidney std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2012-01-12 wgEncodeEM001442 1442 GSM769016 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneKidneyH3k4me3MAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Kidney 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneKidneyH3k4me1MAdult8wksC57bl6StdSig Kidney H3K4m1 adult-8wks H3K4me1 Kidney std ChipSeq ENCODE Mar 2012 Freeze 2011-04-07 2010-11-19 2011-08-18 wgEncodeEM001434 1434 GSM769023 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneKidneyH3k4me1MAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Kidney 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartInputUE14halfC57bl6StdSig Heart 14.5 Input E14.5 Input Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-04 wgEncodeEM002506 2506 GSM1000208 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input U Custom Scripts C57BL/6 wgEncodeLicrHistoneHeartInputUE14halfC57bl6StdSig Signal Embryonic day 14.5 Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Heart E14.5 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartInputMAdult8wksC57bl6StdSig Heart 8w Input adult-8wks Input Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-04-27 2012-01-26 wgEncodeEM001450 1450 GSM769032 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneHeartInputMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Heart 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k79me2MAdult8wksC57bl6StdSig Heart 8w H3K79m2 adult-8wks H3K79me2 Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002639 2639 GSM1000129 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneHeartH3k79me2MAdult8wksC57bl6StdSig Signal Adult 8 weeks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Heart 8w H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k36me3MAdult8wksC57bl6StdSig Heart 8w H3K36m3 adult-8wks H3K36me3 Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002638 2638 GSM1000130 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneHeartH3k36me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Heart 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k27me3MAdult8wksC57bl6StdSig Heart 8w H3K27m3 adult-8wks H3K27me3 Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002637 2637 GSM1000131 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneHeartH3k27me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Heart 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k27acUE14halfC57bl6StdSig Heart 14.5 H3K27a E14.5 H3K27ac Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-04 wgEncodeEM002503 2503 GSM1000137 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrHistoneHeartH3k27acUE14halfC57bl6StdSig Signal Embryonic day 14.5 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. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Heart E14.5 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k27acMAdult8wksC57bl6StdSig Heart 8w H3K27a adult-8wks H3K27ac Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-12-24 2012-09-23 wgEncodeEM002498 2498 GSM1000093 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneHeartH3k27acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Heart 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k09acMAdult8wksC57bl6StdSig Heart 8w H3K9a adult-8wks H3K9ac Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002640 2640 GSM1000149 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneHeartH3k09acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Heart 8w H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k04me3UE14halfC57bl6StdSig Heart 14.5 H3K4m3 E14.5 H3K4me3 Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-04 wgEncodeEM002505 2505 GSM1000135 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrHistoneHeartH3k04me3UE14halfC57bl6StdSig Signal Embryonic day 14.5 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Heart E14.5 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k4me3MAdult8wksC57bl6StdSig Heart 8w H3K4m3 adult-8wks H3K4me3 Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2012-01-12 wgEncodeEM001441 1441 GSM769017 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneHeartH3k4me3MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Heart 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k04me1UE14halfC57bl6StdSig Heart 14.5 H3K4m1 E14.5 H3K4me1 Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-04 wgEncodeEM002504 2504 GSM1000136 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrHistoneHeartH3k04me1UE14halfC57bl6StdSig Signal Embryonic day 14.5 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Heart E14.5 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k4me1MAdult8wksC57bl6StdSig Heart 8w H3K4m1 adult-8wks H3K4me1 Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2010-11-01 2011-08-01 wgEncodeEM001433 1433 GSM769025 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneHeartH3k4me1MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Heart 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEse14H3k36me3ME0129olaStdSig ES-E14 H3K36m3 E0 H3K36me3 ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEM003175 3175 GSM1000125 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts 129/Ola wgEncodeLicrHistoneEse14H3k36me3ME0129olaStdSig Signal Embryonic day 0 (stem cell) Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 E0 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEse14H3k27acME0129olaStdSig ES-E14 H3K27a E0 H3K27ac ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEM003174 3174 GSM1000126 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts 129/Ola wgEncodeLicrHistoneEse14H3k27acME0129olaStdSig Signal Embryonic day 0 (stem cell) 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. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 E0 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEse14H3k09acME0129olaStdSig ES-E14 H3K9a E0 H3K9ac ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-25 2013-03-24 wgEncodeEM003173 3173 GSM1000123 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts 129/Ola wgEncodeLicrHistoneEse14H3k09acME0129olaStdSig Signal Embryonic day 0 (stem cell) 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. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 E0 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEse14H3k04me3ME0129olaStdSig ES-E14 H3K4m3 E0 H3K4me3 ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-24 2013-03-23 wgEncodeEM003172 3172 GSM1000124 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts 129/Ola wgEncodeLicrHistoneEse14H3k04me3ME0129olaStdSig Signal Embryonic day 0 (stem cell) Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 E0 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEse14H3k04me1ME0129olaStdSig ES-E14 H3K4m1 E0 H3K4me1 ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-23 2013-03-22 wgEncodeEM003171 3171 GSM1000121 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts 129/Ola wgEncodeLicrHistoneEse14H3k04me1ME0129olaStdSig Signal Embryonic day 0 (stem cell) Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 E0 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4InputME0C57bl6StdSig ES-Bruce4 Input E0 Input ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-05 wgEncodeEM001683 1683 GSM769010 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneEsb4InputME0C57bl6StdSig Individual Signal Embryonic day 0 (stem cell) mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal ES-Bruce4 E0 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k36me3ME0C57bl6StdSig ES-Bruce4 H3K36m3 E0 H3K36me3 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002710 2710 GSM1000109 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneEsb4H3k36me3ME0C57bl6StdSig Signal Embryonic day 0 (stem cell) Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal ES-Bruce4 E0 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k27me3ME0C57bl6StdSig ES-Bruce4 H3K27m3 E0 H3K27me3 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002709 2709 GSM1000089 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneEsb4H3k27me3ME0C57bl6StdSig Signal Embryonic day 0 (stem cell) 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. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal ES-Bruce4 E0 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k27acME0C57bl6StdSig ES-Bruce4 H3K27a E0 H3K27ac ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-12-24 2012-09-23 wgEncodeEM002497 2497 GSM1000099 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneEsb4H3k27acME0C57bl6StdSig Signal Embryonic day 0 (stem cell) 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. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal ES-Bruce4 E0 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k09me3ME0C57bl6StdSig ES-Bruce4 H3K9m3 E0 H3K9me3 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002721 2721 GSM1000147 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneEsb4H3k09me3ME0C57bl6StdSig Signal Embryonic day 0 (stem cell) 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. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal ES-Bruce4 E0 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k09acME0C57bl6StdSig ES-Bruce4 H3K9a E0 H3K9ac ES-Bruce4 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-27 2013-03-26 wgEncodeEM003176 3176 GSM1000127 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneEsb4H3k09acME0C57bl6StdSig Signal Embryonic day 0 (stem cell) 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. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal ES-Bruce4 E0 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k4me3ME0C57bl6StdSig ES-Bruce4 H3K4m3 E0 H3K4me3 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-05 wgEncodeEM001682 1682 GSM769008 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneEsb4H3k4me3ME0C57bl6StdSig Individual Signal Embryonic day 0 (stem cell) Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal ES-Bruce4 E0 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k4me1ME0C57bl6StdSig ES-Bruce4 H3K4m1 E0 H3K4me1 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001681 1681 GSM769009 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneEsb4H3k4me1ME0C57bl6StdSig Individual Signal Embryonic day 0 (stem cell) Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal ES-Bruce4 E0 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCortexInputMAdult8wksC57bl6StdSig Cortex Input adult-8wks Input Cortex std ChipSeq ENCODE Mar 2012 Freeze 2011-04-27 2012-01-26 wgEncodeEM001449 1449 GSM769019 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneCortexInputMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Cortex Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cortex 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCortexH3k27acMAdult8wksC57bl6StdSig Cortex H3K27a adult-8wks H3K27ac Cortex std ChipSeq ENCODE Mar 2012 Freeze 2011-12-24 2012-09-23 wgEncodeEM002496 2496 GSM1000100 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneCortexH3k27acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Cortex Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Cortex 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCortexH3k4me3MAdult8wksC57bl6StdSig Cortex H3K4m3 adult-8wks H3K4me3 Cortex std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001438 1438 GSM769026 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneCortexH3k4me3MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Cortex Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cortex 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCortexH3k4me1MAdult8wksC57bl6StdSig Cortex H3K4m1 adult-8wks H3K4me1 Cortex std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001437 1437 GSM769022 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneCortexH3k4me1MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Cortex Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cortex 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12InputFImmortalC57bl6StdSig CH12 Input immortalized Input CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-07 2013-03-06 wgEncodeEM003164 3164 GSM1000118 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 input F Custom Scripts C57BL/6 wgEncodeLicrHistoneCh12InputFImmortalC57bl6StdSig Signal Immortal cells B-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal CH12 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k79me2FImmortalC57bl6StdSig CH12 H3K79m2 immortalized H3K79me2 CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-23 2013-03-22 wgEncodeEM003170 3170 GSM1000122 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistoneCh12H3k79me2FImmortalC57bl6StdSig Signal Immortal cells H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). B-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal CH12 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k36me3FImmortalC57bl6StdSig CH12 H3K36m3 immortalized H3K36me3 CH12 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002707 2707 GSM1000091 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistoneCh12H3k36me3FImmortalC57bl6StdSig Signal Immortal cells 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-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal CH12 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k27acFImmortalC57bl6StdSig CH12 H3K27a immortalized H3K27ac CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-22 2013-03-22 wgEncodeEM003167 3167 GSM1000117 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistoneCh12H3k27acFImmortalC57bl6StdSig Signal Immortal cells 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-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal CH12 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k09acFImmortalC57bl6StdSig CH12 H3K9a immortalized H3K9ac CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-22 2013-03-21 wgEncodeEM003169 3169 GSM1000115 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistoneCh12H3k09acFImmortalC57bl6StdSig Signal Immortal cells 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-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal CH12 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k04me3FImmortalC57bl6StdSig CH12 H3K4m3 immortalized H3K4me3 CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-22 2013-03-21 wgEncodeEM003168 3168 GSM1000114 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistoneCh12H3k04me3FImmortalC57bl6StdSig Signal Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal CH12 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k04me2FImmortalC57bl6StdSig CH12 H3K4m2 immortalized H3K4me2 CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-21 2013-03-21 wgEncodeEM003166 3166 GSM1000116 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistoneCh12H3k04me2FImmortalC57bl6StdSig Signal Immortal cells 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-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal CH12 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k04me1FImmortalC57bl6StdSig CH12 H3K4m1 immortalized H3K4me1 CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-20 2013-03-20 wgEncodeEM003165 3165 GSM1000119 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistoneCh12H3k04me1FImmortalC57bl6StdSig Signal Immortal cells Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. B-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal CH12 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCbellumInputMAdult8wksC57bl6StdSig Cbellum Input adult-8wks Input Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2011-04-27 2012-01-26 wgEncodeEM001448 1448 GSM769020 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneCbellumInputMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cerebellum 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCbellumH3k27me3MAdult8wksC57bl6StdSig Cbellum H3K27m3 adult-8wks H3K27me3 Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002708 2708 GSM1000090 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneCbellumH3k27me3MAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Cerebellum 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCbellumH3k27acMAdult8wksC57bl6StdSig Cbellum H3K27a adult-8wks H3K27ac Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2011-12-24 2012-09-23 wgEncodeEM002495 2495 GSM1000097 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneCbellumH3k27acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Cerebellum 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCbellumH3k4me3MAdult8wksC57bl6StdSig Cbellum H3K4m3 adult-8wks H3K4me3 Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2011-01-20 2011-10-20 wgEncodeEM001439 1439 GSM769027 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneCbellumH3k4me3MAdult8wksC57bl6StdSig Both Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue analyzed using replicate samples obtained from and individual and by pooling. Signal Cerebellum 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCbellumH3k4me1MAdult8wksC57bl6StdSig Cbellum H3K4m1 adult-8wks H3K4me1 Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-07 wgEncodeEM001440 1440 GSM769018 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneCbellumH3k4me1MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cerebellum 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBatInputMAdult24wksC57bl6StdSig BAT 24w Input adult-24wks Input BAT std ChipSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEM002656 2656 GSM1000201 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneBatInputMAdult24wksC57bl6StdSig Signal Adult 24 weeks Brown adipocytes tissue Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Brown Adipose Tissue 24w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBatH3k27acMAdult24wksC57bl6StdSig BAT 24w H3K27a adult-24wks H3K27ac BAT std ChipSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEM002653 2653 GSM1000071 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneBatH3k27acMAdult24wksC57bl6StdSig Signal Adult 24 weeks 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. Brown adipocytes tissue Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Brown Adipose Tissue 24w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBatH3k04me3MAdult24wksC57bl6StdSig BAT 24w H3K4m3 adult-24wks H3K4me3 BAT std ChipSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEM002655 2655 GSM1000075 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneBatH3k04me3MAdult24wksC57bl6StdSig Signal Adult 24 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Brown adipocytes tissue Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Brown Adipose Tissue 24w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBatH3k04me1MAdult24wksC57bl6StdSig BAT 24w H3K4m1 adult-24wks H3K4me1 BAT std ChipSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEM002654 2654 GSM1000076 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneBatH3k04me1MAdult24wksC57bl6StdSig Signal Adult 24 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Brown adipocytes tissue Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Brown Adipose Tissue 24w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmdmInputFAdult8wksC57bl6StdSig BMDM Input adult-8wks Input BMDM std ChipSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002660 2660 GSM1000206 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 input F Custom Scripts C57BL/6 wgEncodeLicrHistoneBmdmInputFAdult8wksC57bl6StdSig Signal Adult 8 weeks Bone marrow derived macrophage Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal BMDM 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmdmH3k27acFAdult8wksC57bl6StdSig BMDM H3K27a adult-8wks H3K27ac BMDM std ChipSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002657 2657 GSM1000074 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistoneBmdmH3k27acFAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Bone marrow derived macrophage Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal BMDM 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmdmH3k04me3FAdult8wksC57bl6StdSig BMDM H3K4m3 adult-8wks H3K4me3 BMDM std ChipSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002659 2659 GSM1000065 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistoneBmdmH3k04me3FAdult8wksC57bl6StdSig Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Bone marrow derived macrophage Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal BMDM 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmdmH3k04me1FAdult8wksC57bl6StdSig BMDM H3K4m1 adult-8wks H3K4me1 BMDM std ChipSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002658 2658 GSM1000066 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrHistoneBmdmH3k04me1FAdult8wksC57bl6StdSig Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Bone marrow derived macrophage Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal BMDM 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmarrowInputMAdult8wksC57bl6StdSig BoneMarrow Input adult-8wks Input BoneMarrow std ChipSeq ENCODE Mar 2012 Freeze 2011-04-27 2012-01-26 wgEncodeEM001447 1447 GSM769011 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneBmarrowInputMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Bone Marrow Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Bone Marrow 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmarrowH3k27acMAdult8wksC57bl6StdSig BoneMarrow H3K27a adult-8wks H3K27ac BoneMarrow std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-23 wgEncodeEM002478 2478 GSM1000108 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneBmarrowH3k27acMAdult8wksC57bl6StdSig Signal Adult 8 weeks 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. Bone Marrow Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Bone Marrow 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmarrowH3k4me3MAdult8wksC57bl6StdSig BoneMarrow H3K4m3 adult-8wks H3K4me3 BoneMarrow std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001436 1436 GSM769021 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneBmarrowH3k4me3MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Bone Marrow Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Bone Marrow 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmarrowH3k4me1MAdult8wksC57bl6StdSig BoneMarrow H3K4m1 adult-8wks H3K4me1 BoneMarrow std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001435 1435 GSM769024 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneBmarrowH3k4me1MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Bone Marrow Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Bone Marrow 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBcellcd43nInputMAdult8wksC57bl6StdSig BCD43- Input adult-8wks Input B-cell_(CD43-) std ChipSeq ENCODE Jul 2012 Freeze 2012-05-25 2013-02-25 wgEncodeEM003163 3163 GSM1000120 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 input M Custom Scripts C57BL/6 wgEncodeLicrHistoneBcellcd43nInputMAdult8wksC57bl6StdSig Signal Adult 8 weeks mouse spleen B cells, CD43-,CD11b- Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal B-cell (CD43-) 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBcellcd43nH3k36me3MAdlt8wC57bl6StdSig BCD43- H3K36m3 adult-8wks H3K36me3 B-cell_(CD43-) std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002720 2720 GSM1000148 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneBcellcd43nH3k36me3MAdlt8wC57bl6StdSig Signal Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. mouse spleen B cells, CD43-,CD11b- Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal B-cell (CD43-) 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBcellcd43nH3k27me3MAdlt8wC57bl6StdSig BCD43- H3K27m3 adult-8wks H3K27me3 B-cell_(CD43-) std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002719 2719 GSM1000088 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrHistoneBcellcd43nH3k27me3MAdlt8wC57bl6StdSig Signal Adult 8 weeks 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. mouse spleen B cells, CD43-,CD11b- Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal B-cell (CD43-) 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneViewPeaks Peaks Histone Mods by ChIP-seq from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainH3k36me3ME14halfC57bl6StdPk Brain H3K36m3 E14.5 H3K36me3 WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002718 2718 GSM1000072 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneWbrainH3k36me3ME14halfC57bl6StdPk Peaks Embryonic day 14.5 Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Whole Brain E14.5 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainH3k27me3ME14halfC57bl6StdPk Brain H3K27m3 E14.5 H3K27me3 WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002725 2725 GSM1000143 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneWbrainH3k27me3ME14halfC57bl6StdPk Peaks Embryonic day 14.5 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. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Whole Brain E14.5 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainH3k27acUE14halfC57bl6StdPk Brain H3K27a E14.5 H3K27ac WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002491 2491 GSM1000094 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrHistoneWbrainH3k27acUE14halfC57bl6StdPk Peaks Embryonic day 14.5 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. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Whole Brain E14.5 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainH3k09me3ME14halfC57bl6StdPk Brain H3K9m3 E14.5 H3K9me3 WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002726 2726 GSM1000106 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneWbrainH3k09me3ME14halfC57bl6StdPk Peaks Embryonic day 14.5 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. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Whole Brain E14.5 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainH3k04me3UE14halfC57bl6StdPk Brain H3K4m3 E14.5 H3K4me3 WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002493 2493 GSM1000095 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrHistoneWbrainH3k04me3UE14halfC57bl6StdPk Peaks Embryonic day 14.5 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Whole Brain E14.5 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneWbrainH3k04me1UE14halfC57bl6StdPk Brain H3K4m1 E14.5 H3K4me1 WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002492 2492 GSM1000096 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrHistoneWbrainH3k04me1UE14halfC57bl6StdPk Peaks Embryonic day 14.5 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Whole Brain E14.5 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneThymusH3k36me3MAdult8wksC57bl6StdPk Thymus H3K36m3 adult-8wks H3K36me3 Thymus std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEM002717 2717 GSM1000068 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneThymusH3k36me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Thymus 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneThymusH3k27me3MAdlt8wC57bl6StdPk Thymus H3K27m3 adult-8wks H3K27me3 Thymus std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002724 2724 GSM1000144 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneThymusH3k27me3MAdlt8wC57bl6StdPk Peaks Adult 8 weeks 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. Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Thymus 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneThymusH3k27acMAdult8wksC57bl6StdPk Thymus H3K27a adult-8wks H3K27ac Thymus std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002474 2474 GSM1000103 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneThymusH3k27acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Thymus 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneThymusH3k04me3MAdult8wksC57bl6StdPk Thymus H3K4m3 adult-8wks H3K4me3 Thymus std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002476 2476 GSM1000101 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneThymusH3k04me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Thymus 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneThymusH3k04me1MAdult8wksC57bl6StdPk Thymus H3K4m1 adult-8wks H3K4me1 Thymus std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002475 2475 GSM1000102 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneThymusH3k04me1MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Thymus 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneTestisH3k36me3MAdult8wksC57bl6StdPk Testis H3K36m3 adult-8wks H3K36me3 Testis std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002716 2716 GSM1000067 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneTestisH3k36me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Testis 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneTestisH3k27me3MAdlt8wC57bl6StdPk Testis H3K27m3 adult-8wks H3K27me3 Testis std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002723 2723 GSM1000145 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneTestisH3k27me3MAdlt8wC57bl6StdPk Peaks Adult 8 weeks 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. Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Testis 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneTestisH3k27acMAdult8wksC57bl6StdPk Testis H3K27a adult-8wks H3K27ac Testis std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002487 2487 GSM1000081 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneTestisH3k27acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Testis 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneTestisH3k04me3MAdult8wksC57bl6StdPk Testis H3K4m3 adult-8wks H3K4me3 Testis std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002489 2489 GSM1000079 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneTestisH3k04me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Testis 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneTestisH3k04me1MAdult8wksC57bl6StdPk Testis H3K4m1 adult-8wks H3K4me1 Testis std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002488 2488 GSM1000078 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneTestisH3k04me1MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Testis 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSpleenH3k36me3MAdult8wksC57bl6StdPk Spleen H3K36m3 adult-8wks H3K36me3 Spleen std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEM002715 2715 GSM1000070 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneSpleenH3k36me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Spleen 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSpleenH3k27me3MAdlt8wC57bl6StdPk Spleen H3K27m3 adult-8wks H3K27me3 Spleen std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002722 2722 GSM1000146 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneSpleenH3k27me3MAdlt8wC57bl6StdPk Peaks Adult 8 weeks 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. Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Spleen 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSpleenH3k27acMAdult8wksC57bl6StdPk Spleen H3K27a adult-8wks H3K27ac Spleen std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002502 2502 GSM1000138 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneSpleenH3k27acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Spleen 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSpleenH3k4me3MAdult8wksC57bl6StdPk Spleen H3K4m3 adult-8wks H3K4me3 Spleen std ChipSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-01 wgEncodeEM001458 1458 GSM769036 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneSpleenH3k4me3MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Spleen 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSpleenH3k4me1MAdult8wksC57bl6StdPk Spleen H3K4m1 adult-8wks H3K4me1 Spleen std ChipSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-01 wgEncodeEM001457 1457 GSM769031 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneSpleenH3k4me1MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Spleen 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSmintH3k36me3MAdult8wksC57bl6StdPk SmInt H3K36m3 adult-8wks H3K36me3 SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002714 2714 GSM1000069 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneSmintH3k36me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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 Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Small Intestine 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSmintH3k27me3MAdult8wksC57bl6StdPk SmInt H3K27m3 adult-8wks H3K27me3 SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002713 2713 GSM1000064 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneSmintH3k27me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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 Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Small Intestine 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSmintH3k27acMAdult8wksC57bl6StdPk SmInt H3K27a adult-8wks H3K27ac SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002483 2483 GSM1000084 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneSmintH3k27acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Small Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Small Intestine 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSmintH3k04me3MAdult8wksC57bl6StdPk SmInt H3K4m3 adult-8wks H3K4me3 SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002485 2485 GSM1000083 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneSmintH3k04me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Small Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Small Intestine 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneSmintH3k04me1MAdult8wksC57bl6StdPk SmInt H3K4m1 adult-8wks H3K4me1 SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002484 2484 GSM1000082 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneSmintH3k04me1MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Small Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Small Intestine 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistonePlacH3k27acFAdult8wksC57bl6StdPk Placenta H3K27a adult-8wks H3K27ac Placenta std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002507 2507 GSM1000134 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistonePlacH3k27acFAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Placenta Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Placenta 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistonePlacH3k04me3FAdult8wksC57bl6StdPk Placenta H3K4m3 adult-8wks H3K4me3 Placenta std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002509 2509 GSM1000132 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistonePlacH3k04me3FAdult8wksC57bl6StdPk Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Placenta Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Placenta 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistonePlacH3k04me1FAdult8wksC57bl6StdPk Placenta H3K4m1 adult-8wks H3K4me1 Placenta std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002508 2508 GSM1000133 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistonePlacH3k04me1FAdult8wksC57bl6StdPk Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Placenta Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Placenta 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneOlfactH3k27acMAdult8wksC57bl6StdPk Olfact H3K27a adult-8wks H3K27ac OlfactBulb std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002471 2471 GSM1000105 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Peaks C57BL/6 wgEncodeLicrHistoneOlfactH3k27acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Olfactory Bulb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Olfactory Bulb 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneOlfactH3k04me3MAdult8wksC57bl6StdPk Olfact H3K4m3 adult-8wks H3K4me3 OlfactBulb std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002511 2511 GSM1000128 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneOlfactH3k04me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Olfactory Bulb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Olfactory Bulb 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneOlfactH3k04me1MAdult8wksC57bl6StdPk Olfact H3K4m1 adult-8wks H3K4me1 OlfactBulb std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002472 2472 GSM1000104 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Peaks C57BL/6 wgEncodeLicrHistoneOlfactH3k04me1MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Olfactory Bulb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Olfactory Bulb 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k79me2MImmortalC57bl6StdPk MEL H3K79m2 immortalized H3K79me2 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002647 2647 GSM1000156 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS Unknown wgEncodeLicrHistoneMelH3k79me2MImmortalC57bl6StdPk Peaks Immortal cells H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Regions of enriched signal in experiment MEL H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k36me3MImmortalC57bl6StdPk MEL H3K36m3 immortalized H3K36me3 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002646 2646 GSM1000155 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS Unknown wgEncodeLicrHistoneMelH3k36me3MImmortalC57bl6StdPk Peaks Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Regions of enriched signal in experiment MEL H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k27me3MImmortalC57bl6StdPk MEL H3K27m3 immortalized H3K27me3 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002645 2645 GSM1000154 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS Unknown wgEncodeLicrHistoneMelH3k27me3MImmortalC57bl6StdPk Peaks Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Regions of enriched signal in experiment MEL H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k27acMImmortalC57bl6StdPk MEL H3K27a immortalized H3K27ac MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-28 wgEncodeEM002649 2649 GSM1000142 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS Unknown wgEncodeLicrHistoneMelH3k27acMImmortalC57bl6StdPk Peaks Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Regions of enriched signal in experiment MEL H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k09acMImmortalC57bl6StdPk MEL H3K9a immortalized H3K9ac MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002648 2648 GSM1000141 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS Unknown wgEncodeLicrHistoneMelH3k09acMImmortalC57bl6StdPk Peaks Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Regions of enriched signal in experiment MEL H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k04me3MImmortalC57bl6StdPk MEL H3K4m3 immortalized H3K4me3 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-28 wgEncodeEM002651 2651 GSM1000087 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS Unknown wgEncodeLicrHistoneMelH3k04me3MImmortalC57bl6StdPk Peaks Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Regions of enriched signal in experiment MEL H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMelH3k04me1MImmortalC57bl6StdPk MEL H3K4m1 immortalized H3K4me1 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-28 wgEncodeEM002650 2650 GSM1000073 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS Unknown wgEncodeLicrHistoneMelH3k04me1MImmortalC57bl6StdPk Peaks Immortal cells Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Regions of enriched signal in experiment MEL H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMefH3k27acMAdult8wksC57bl6StdPk MEF H3K27a adult-8wks H3K27ac MEF std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002501 2501 GSM1000139 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneMefH3k27acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Mouse Embryonic Fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment MEF 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMefH3k4me3MAdult8wksC57bl6StdPk MEF H3K4m3 adult-8wks H3K4me3 MEF std ChipSeq ENCODE Mar 2012 Freeze 2011-04-29 2012-01-28 wgEncodeEM001455 1455 GSM769029 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneMefH3k4me3MAdult8wksC57bl6StdPk Individual Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Mouse Embryonic Fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment MEF 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneMefH3k4me1MAdult8wksC57bl6StdPk MEF H3K4m1 adult-8wks H3K4me1 MEF std ChipSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEM001454 1454 GSM769028 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneMefH3k4me1MAdult8wksC57bl6StdPk Individual Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Mouse Embryonic Fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment MEF 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLungH3k4me3MAdult8wksC57bl6StdPk Lung H3K4m3 adult-8wks H3K4me3 Lung std ChipSeq ENCODE Mar 2012 Freeze 2011-04-15 2012-01-14 wgEncodeEM001446 1446 GSM769012 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneLungH3k4me3MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Lung Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Lung 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLungH3k4me1MAdult8wksC57bl6StdPk Lung H3K4m1 adult-8wks H3K4me1 Lung std ChipSeq ENCODE Mar 2012 Freeze 2011-04-15 2012-01-14 wgEncodeEM001445 1445 GSM769013 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneLungH3k4me1MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Lung Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Lung 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k79me2MAdult8wksC57bl6StdPk Liver 8w H3K79m2 adult-8wks H3K79me2 Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002643 2643 GSM1000152 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneLiverH3k79me2MAdult8wksC57bl6StdPk Peaks Adult 8 weeks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Liver 8w H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k36me3MAdult8wksC57bl6StdPk Liver 8w H3K36m3 adult-8wks H3K36me3 Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002642 2642 GSM1000151 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneLiverH3k36me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Liver 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k27me3MAdult8wksC57bl6StdPk Liver 8w H3K27m3 adult-8wks H3K27me3 Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002641 2641 GSM1000150 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneLiverH3k27me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Liver 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k27acUE14halfC57bl6StdPk Liver 14.5 H3K27a E14.5 H3K27ac Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002571 2571 GSM1000113 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrHistoneLiverH3k27acUE14halfC57bl6StdPk Peaks Embryonic day 14.5 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. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Liver E14.5 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k27acMAdult8wksC57bl6StdPk Liver 8w H3K27a adult-8wks H3K27ac Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002500 2500 GSM1000140 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneLiverH3k27acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Liver 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k09acMAdult8wksC57bl6StdPk Liver 8w H3K9a adult-8wks H3K9ac Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002644 2644 GSM1000153 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneLiverH3k09acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Liver 8w H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k04me3UE14halfC57bl6StdPk Liver 14.5 H3K4m3 E14.5 H3K4me3 Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002572 2572 GSM1000110 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrHistoneLiverH3k04me3UE14halfC57bl6StdPk Peaks Embryonic day 14.5 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Liver E14.5 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k4me3MAdult8wksC57bl6StdPk Liver 8w H3K4m3 adult-8wks H3K4me3 Liver std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2012-01-12 wgEncodeEM001444 1444 GSM769014 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneLiverH3k4me3MAdult8wksC57bl6StdPk Individual Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Liver 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k04me1UE14halfC57bl6StdPk Liver 14.5 H3K4m1 E14.5 H3K4me1 Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002573 2573 GSM1000111 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrHistoneLiverH3k04me1UE14halfC57bl6StdPk Peaks Embryonic day 14.5 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Liver E14.5 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLiverH3k4me1MAdult8wksC57bl6StdPk Liver 8w H3K4m1 adult-8wks H3K4me1 Liver std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2012-01-12 wgEncodeEM001443 1443 GSM769015 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneLiverH3k4me1MAdult8wksC57bl6StdPk Individual Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Liver 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLimbH3k27acUE14halfC57bl6StdPk Limb H3K27a E14.5 H3K27ac Limb std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002479 2479 GSM1000107 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrHistoneLimbH3k27acUE14halfC57bl6StdPk Peaks Embryonic day 14.5 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. Limb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Limb E14.5 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLimbH3k04me3UE14halfC57bl6StdPk Limb H3K4m3 E14.5 H3K4me3 Limb std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002481 2481 GSM1000086 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrHistoneLimbH3k04me3UE14halfC57bl6StdPk Peaks Embryonic day 14.5 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Limb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Limb E14.5 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneLimbH3k04me1UE14halfC57bl6StdPk Limb H3K4m1 E14.5 H3K4me1 Limb std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002480 2480 GSM1000085 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrHistoneLimbH3k04me1UE14halfC57bl6StdPk Peaks Embryonic day 14.5 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Limb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Limb E14.5 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneKidneyH3k36me3MAdult8wksC57bl6StdPk Kidney H3K36m3 adult-8wks H3K36me3 Kidney std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002712 2712 GSM1000063 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneKidneyH3k36me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Kidney 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneKidneyH3k27me3MAdult8wksC57bl6StdPk Kidney H3K27m3 adult-8wks H3K27me3 Kidney std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002711 2711 GSM1000077 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneKidneyH3k27me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Kidney 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneKidneyH3k27acMAdult8wksC57bl6StdPk Kidney H3K27a adult-8wks H3K27ac Kidney std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002499 2499 GSM1000092 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneKidneyH3k27acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Kidney 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneKidneyH3k4me3MAdult8wksC57bl6StdPk Kidney H3K4m3 adult-8wks H3K4me3 Kidney std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2012-01-12 wgEncodeEM001442 1442 GSM769016 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneKidneyH3k4me3MAdult8wksC57bl6StdPk Individual Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Kidney 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneKidneyH3k4me1MAdult8wksC57bl6StdPk Kidney H3K4m1 adult-8wks H3K4me1 Kidney std ChipSeq ENCODE Mar 2012 Freeze 2011-04-07 2010-11-19 2011-08-18 wgEncodeEM001434 1434 GSM769023 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneKidneyH3k4me1MAdult8wksC57bl6StdPk Individual Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Kidney 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k79me2MAdult8wksC57bl6StdPk Heart 8w H3K79m2 adult-8wks H3K79me2 Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002639 2639 GSM1000129 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneHeartH3k79me2MAdult8wksC57bl6StdPk Peaks Adult 8 weeks H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Heart 8w H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k36me3MAdult8wksC57bl6StdPk Heart 8w H3K36m3 adult-8wks H3K36me3 Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002638 2638 GSM1000130 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneHeartH3k36me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Heart 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k27me3MAdult8wksC57bl6StdPk Heart 8w H3K27m3 adult-8wks H3K27me3 Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002637 2637 GSM1000131 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneHeartH3k27me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Heart 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k27acUE14halfC57bl6StdPk Heart 14.5 H3K27a E14.5 H3K27ac Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002503 2503 GSM1000137 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrHistoneHeartH3k27acUE14halfC57bl6StdPk Peaks Embryonic day 14.5 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. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Heart E14.5 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k27acMAdult8wksC57bl6StdPk Heart 8w H3K27a adult-8wks H3K27ac Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002498 2498 GSM1000093 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneHeartH3k27acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Heart 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k09acMAdult8wksC57bl6StdPk Heart 8w H3K9a adult-8wks H3K9ac Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002640 2640 GSM1000149 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneHeartH3k09acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Heart 8w H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k04me3UE14halfC57bl6StdPk Heart 14.5 H3K4m3 E14.5 H3K4me3 Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002505 2505 GSM1000135 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrHistoneHeartH3k04me3UE14halfC57bl6StdPk Peaks Embryonic day 14.5 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Heart E14.5 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k4me3MAdult8wksC57bl6StdPk Heart 8w H3K4m3 adult-8wks H3K4me3 Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2012-01-12 wgEncodeEM001441 1441 GSM769017 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneHeartH3k4me3MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Heart 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k04me1UE14halfC57bl6StdPk Heart 14.5 H3K4m1 E14.5 H3K4me1 Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002504 2504 GSM1000136 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrHistoneHeartH3k04me1UE14halfC57bl6StdPk Peaks Embryonic day 14.5 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Heart E14.5 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneHeartH3k4me1MAdult8wksC57bl6StdPk Heart 8w H3K4m1 adult-8wks H3K4me1 Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2010-11-01 2011-08-01 wgEncodeEM001433 1433 GSM769025 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneHeartH3k4me1MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Heart 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEse14H3k36me3ME0129olaStdPk ES-E14 H3K36m3 E0 H3K36me3 ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEM003175 3175 GSM1000125 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS 129/Ola wgEncodeLicrHistoneEse14H3k36me3ME0129olaStdPk Peaks Embryonic day 0 (stem cell) Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 E0 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEse14H3k27acME0129olaStdPk ES-E14 H3K27a E0 H3K27ac ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-26 2013-03-26 wgEncodeEM003174 3174 GSM1000126 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS 129/Ola wgEncodeLicrHistoneEse14H3k27acME0129olaStdPk Peaks Embryonic day 0 (stem cell) 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. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 E0 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEse14H3k09acME0129olaStdPk ES-E14 H3K9a E0 H3K9ac ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-25 2013-03-24 wgEncodeEM003173 3173 GSM1000123 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS 129/Ola wgEncodeLicrHistoneEse14H3k09acME0129olaStdPk Peaks Embryonic day 0 (stem cell) 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. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 E0 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEse14H3k04me3ME0129olaStdPk ES-E14 H3K4m3 E0 H3K4me3 ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-24 2013-03-23 wgEncodeEM003172 3172 GSM1000124 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS 129/Ola wgEncodeLicrHistoneEse14H3k04me3ME0129olaStdPk Peaks Embryonic day 0 (stem cell) Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 E0 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEse14H3k04me1ME0129olaStdPk ES-E14 H3K4m1 E0 H3K4me1 ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-23 2013-03-22 wgEncodeEM003171 3171 GSM1000121 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS 129/Ola wgEncodeLicrHistoneEse14H3k04me1ME0129olaStdPk Peaks Embryonic day 0 (stem cell) Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 E0 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k36me3ME0C57bl6StdPk ES-Bruce4 H3K36m3 E0 H3K36me3 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002710 2710 GSM1000109 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneEsb4H3k36me3ME0C57bl6StdPk Peaks Embryonic day 0 (stem cell) Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment ES-Bruce4 E0 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k27me3ME0C57bl6StdPk ES-Bruce4 H3K27m3 E0 H3K27me3 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002709 2709 GSM1000089 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneEsb4H3k27me3ME0C57bl6StdPk Peaks Embryonic day 0 (stem cell) 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. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment ES-Bruce4 E0 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k27acME0C57bl6StdPk ES-Bruce4 H3K27a E0 H3K27ac ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002497 2497 GSM1000099 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneEsb4H3k27acME0C57bl6StdPk Peaks Embryonic day 0 (stem cell) 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. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment ES-Bruce4 E0 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k09me3ME0C57bl6StdPk ES-Bruce4 H3K9m3 E0 H3K9me3 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002721 2721 GSM1000147 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneEsb4H3k09me3ME0C57bl6StdPk Peaks Embryonic day 0 (stem cell) 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. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment ES-Bruce4 E0 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k09acME0C57bl6StdPk ES-Bruce4 H3K9a E0 H3K9ac ES-Bruce4 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-27 2013-03-26 wgEncodeEM003176 3176 GSM1000127 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneEsb4H3k09acME0C57bl6StdPk Peaks Embryonic day 0 (stem cell) 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. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment ES-Bruce4 E0 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k4me3ME0C57bl6StdPk ES-Bruce4 H3K4m3 E0 H3K4me3 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-05 wgEncodeEM001682 1682 GSM769008 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneEsb4H3k4me3ME0C57bl6StdPk Individual Peaks Embryonic day 0 (stem cell) Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment ES-Bruce4 E0 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneEsb4H3k4me1ME0C57bl6StdPk ES-Bruce4 H3K4m1 E0 H3K4me1 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001681 1681 GSM769009 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneEsb4H3k4me1ME0C57bl6StdPk Individual Peaks Embryonic day 0 (stem cell) Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment ES-Bruce4 E0 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCortexH3k27acMAdult8wksC57bl6StdPk Cortex H3K27a adult-8wks H3K27ac Cortex std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002496 2496 GSM1000100 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneCortexH3k27acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Cortex Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Cortex 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCortexH3k4me3MAdult8wksC57bl6StdPk Cortex H3K4m3 adult-8wks H3K4me3 Cortex std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001438 1438 GSM769026 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneCortexH3k4me3MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Cortex Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Cortex 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCortexH3k4me1MAdult8wksC57bl6StdPk Cortex H3K4m1 adult-8wks H3K4me1 Cortex std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001437 1437 GSM769022 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneCortexH3k4me1MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Cortex Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Cortex 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k79me2FImmortalC57bl6StdPk CH12 H3K79m2 immortalized H3K79me2 CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-23 2013-03-22 wgEncodeEM003170 3170 GSM1000122 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistoneCh12H3k79me2FImmortalC57bl6StdPk Peaks Immortal cells H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3). B-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment CH12 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k36me3FImmortalC57bl6StdPk CH12 H3K36m3 immortalized H3K36me3 CH12 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002707 2707 GSM1000091 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistoneCh12H3k36me3FImmortalC57bl6StdPk Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment CH12 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k27acFImmortalC57bl6StdPk CH12 H3K27a immortalized H3K27ac CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-22 2013-03-22 wgEncodeEM003167 3167 GSM1000117 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistoneCh12H3k27acFImmortalC57bl6StdPk Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment CH12 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k09acFImmortalC57bl6StdPk CH12 H3K9a immortalized H3K9ac CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-22 2013-03-21 wgEncodeEM003169 3169 GSM1000115 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistoneCh12H3k09acFImmortalC57bl6StdPk Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment CH12 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k04me3FImmortalC57bl6StdPk CH12 H3K4m3 immortalized H3K4me3 CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-22 2013-03-21 wgEncodeEM003168 3168 GSM1000114 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistoneCh12H3k04me3FImmortalC57bl6StdPk Peaks Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment CH12 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k04me2FImmortalC57bl6StdPk CH12 H3K4m2 immortalized H3K4me2 CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-21 2013-03-21 wgEncodeEM003166 3166 GSM1000116 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistoneCh12H3k04me2FImmortalC57bl6StdPk Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment CH12 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCh12H3k04me1FImmortalC57bl6StdPk CH12 H3K4m1 immortalized H3K4me1 CH12 std ChipSeq ENCODE Jul 2012 Freeze 2012-06-20 2013-03-20 wgEncodeEM003165 3165 GSM1000119 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistoneCh12H3k04me1FImmortalC57bl6StdPk Peaks Immortal cells Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. B-cell lymphoma (GM12878 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment CH12 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCbellumH3k27me3MAdult8wksC57bl6StdPk Cbellum H3K27m3 adult-8wks H3K27me3 Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-30 wgEncodeEM002708 2708 GSM1000090 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneCbellumH3k27me3MAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Cerebellum 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCbellumH3k27acMAdult8wksC57bl6StdPk Cbellum H3K27a adult-8wks H3K27ac Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002495 2495 GSM1000097 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneCbellumH3k27acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Cerebellum 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCbellumH3k4me3MAdult8wksC57bl6StdPk Cbellum H3K4m3 adult-8wks H3K4me3 Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2011-01-20 2011-10-20 wgEncodeEM001439 1439 GSM769027 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneCbellumH3k4me3MAdult8wksC57bl6StdPk Both Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue analyzed using replicate samples obtained from and individual and by pooling. Regions of enriched signal in experiment Cerebellum 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneCbellumH3k4me1MAdult8wksC57bl6StdPk Cbellum H3K4m1 adult-8wks H3K4me1 Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2011-03-08 2011-12-07 wgEncodeEM001440 1440 GSM769018 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneCbellumH3k4me1MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Cerebellum 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBatH3k27acMAdult24wksC57bl6StdPk BAT 24w H3K27a adult-24wks H3K27ac BAT std ChipSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEM002653 2653 GSM1000071 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneBatH3k27acMAdult24wksC57bl6StdPk Peaks Adult 24 weeks 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. Brown adipocytes tissue Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Brown Adipose Tissue 24w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBatH3k04me3MAdult24wksC57bl6StdPk BAT 24w H3K4m3 adult-24wks H3K4me3 BAT std ChipSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEM002655 2655 GSM1000075 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneBatH3k04me3MAdult24wksC57bl6StdPk Peaks Adult 24 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Brown adipocytes tissue Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Brown Adipose Tissue 24w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBatH3k04me1MAdult24wksC57bl6StdPk BAT 24w H3K4m1 adult-24wks H3K4me1 BAT std ChipSeq ENCODE Mar 2012 Freeze 2012-03-01 2012-11-29 wgEncodeEM002654 2654 GSM1000076 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneBatH3k04me1MAdult24wksC57bl6StdPk Peaks Adult 24 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Brown adipocytes tissue Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Brown Adipose Tissue 24w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmdmH3k27acFAdult8wksC57bl6StdPk BMDM H3K27a adult-8wks H3K27ac BMDM std ChipSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002657 2657 GSM1000074 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistoneBmdmH3k27acFAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Bone marrow derived macrophage Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment BMDM 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmdmH3k04me3FAdult8wksC57bl6StdPk BMDM H3K4m3 adult-8wks H3K4me3 BMDM std ChipSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002659 2659 GSM1000065 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistoneBmdmH3k04me3FAdult8wksC57bl6StdPk Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Bone marrow derived macrophage Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment BMDM 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmdmH3k04me1FAdult8wksC57bl6StdPk BMDM H3K4m1 adult-8wks H3K4me1 BMDM std ChipSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002658 2658 GSM1000066 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrHistoneBmdmH3k04me1FAdult8wksC57bl6StdPk Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Bone marrow derived macrophage Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment BMDM 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmarrowH3k27acMAdult8wksC57bl6StdPk BoneMarrow H3K27a adult-8wks H3K27ac BoneMarrow std ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-13 wgEncodeEM002478 2478 GSM1000108 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneBmarrowH3k27acMAdult8wksC57bl6StdPk Peaks Adult 8 weeks 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. Bone Marrow Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Bone Marrow 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmarrowH3k4me3MAdult8wksC57bl6StdPk BoneMarrow H3K4m3 adult-8wks H3K4me3 BoneMarrow std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001436 1436 GSM769021 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneBmarrowH3k4me3MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Bone Marrow Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Bone Marrow 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBmarrowH3k4me1MAdult8wksC57bl6StdPk BoneMarrow H3K4m1 adult-8wks H3K4me1 BoneMarrow std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001435 1435 GSM769024 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrHistoneBmarrowH3k4me1MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Bone Marrow Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Bone Marrow 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBcellcd43nH3k36me3MAdlt8wC57bl6StdPk BCD43- H3K36m3 adult-8wks H3K36me3 B-cell_(CD43-) std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002720 2720 GSM1000148 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneBcellcd43nH3k36me3MAdlt8wC57bl6StdPk Peaks Adult 8 weeks Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. mouse spleen B cells, CD43-,CD11b- Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment B-cell (CD43-) 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrHistoneBcellcd43nH3k27me3MAdlt8wC57bl6StdPk BCD43- H3K27m3 adult-8wks H3K27me3 B-cell_(CD43-) std ChipSeq ENCODE Mar 2012 Freeze 2012-03-31 2012-12-30 wgEncodeEM002719 2719 GSM1000088 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrHistoneBcellcd43nH3k27me3MAdlt8wC57bl6StdPk Peaks Adult 8 weeks 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. mouse spleen B cells, CD43-,CD11b- Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment B-cell (CD43-) 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeq LICR RNA-seq GSE36026 RNA-seq from ENCODE/LICR Expression and Regulation Description Using RNA-seq (Mortazavi et al., 2008), high-resolution genome-wide maps of the mouse transcriptome in various mouse (C57BL/6) tissues, primary cells, cell lines of different developmental stage and age groups were generated. Display Conventions and Configuration This is a composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring composite tracks are here. This track contains the following views: SignalDensity graph (wiggle) of signal enrichment based on processed data. AlignmentsMappings of short reads to the genome. See the SAM Format Specification for more information on the SAM/BAM file format. 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 Cells were grown according to the approved ENCODE cell culture protocols. RNA-seq RNA samples from tissues and primary cells were extracted from Trizol&#174; according to protocol (Invitrogen). Long PolyA+ RNA was purified with the Dynabeads mRNA purification kit (Invitrogen). The mRNA libraries were prepared for strand-specific sequencing as described previously (Parkhomchuk et al., 2009). Sequencing and Analysis Samples were sequenced on Illumina Genome Analyzer II, Genome Analyzer IIx and HiSeq 2000 platforms for 36 cycles. Image analysis, base calling and alignment to the mouse genome version NCBI37/mm9 were performed using Illumina&#39;s RTA. Alignment to the mouse genome was performed using TopHat (Trapnell et al., 2009). Wig files were generated by TopHat and expression levels were calculated with Cufflinks (Trapnell et al., 2010). Release Notes This is Release 2 (Mar 2012). It contains a total of 22 RNA-seq experiments with the addition of 12 new experiments. Credits These data were generated and analyzed in Bing Ren&#39;s laboratory at the Ludwig Institute for Cancer Research. Contact: Yin Shen References 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. PMID: 18516045 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. PMID: 19620212; PMC: PMC2764448 Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. PMID: 19289445; PMC: PMC2672628 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. PMID: 20436464; PMC: PMC3146043 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. 
wgEncodeLicrRnaSeqViewSignal sgnal RNA-seq from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6SigRep2 Brain E14.5 Sg 2 E14.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002390 2390 GSM929723 Ren LICR-m 11/10/10 Lane 5 cell 1x36 2 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6SigRep2 Individual Signal Embryonic day 14.5 Whole Brain Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6SigRep1 Brain E14.5 Sg 1 E14.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002390 2390 GSM929723 Ren LICR-m 11/10/10 Lane 5 cell 1x36 1 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6SigRep1 Individual Signal Embryonic day 14.5 Whole Brain Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6SigRep2 Thymus 8wk Sg 2 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-20 wgEncodeEM002386 2386 GSM929714 Ren LICR-m 10/13/10 Lane 6 cell 1x36 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Thymus Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Thymus Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6SigRep1 Thymus 8wk Sg 1 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-20 wgEncodeEM002386 2386 GSM929714 Ren LICR-m 10/13/10 Lane 6 cell 1x36 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Thymus Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Thymus Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6SigRep2 Testis 8wk Sg 2 adult-8wks Testis RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002389 2389 GSM929715 Ren LICR-m 10/13/10 Lane 5 cell 1x36 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Testis Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Testis Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6SigRep1 Testis 8wk Sg 1 adult-8wks Testis RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002389 2389 GSM929715 Ren LICR-m 10/13/10 Lane 5 cell 1x36 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Testis Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Testis Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6SigRep2 Spleen 8wk Sg 2 adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001709 1709 GSM929720 Ren LICR-m 03/10/10 Lane 4 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Spleen Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Spleen Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6SigRep1 Spleen 8wk Sg 1 adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001709 1709 GSM929720 Ren LICR-m 03/10/10 Lane 3 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Spleen Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Spleen Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6SigRep2 SmInt 8wk Sg 2 adult-8wks SmIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002388 2388 GSM929716 Ren LICR-m 11/4/10 Lane 6 cell 1x36 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Small Intestine Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Small Intestine Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6SigRep1 SmInt 8wk Sg 1 adult-8wks SmIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002388 2388 GSM929716 Ren LICR-m 11/4/10 Lane 6 cell 1x36 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Small Intestine Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Small Intestine Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6SigRep2 Placenta 8wk Sg 2 adult-8wks Placenta RnaSeq ENCODE Mar 2012 Freeze 2012-01-06 2012-10-05 wgEncodeEM002393 2393 GSM929722 Ren LICR-m 10/13/10 Lane 4 cell 1x36 2 longPolyA Illumina_HiSeq_2000 F TopHat C57BL/6 wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Placenta Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Placenta Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6SigRep1 Placenta 8wk Sg 1 adult-8wks Placenta RnaSeq ENCODE Mar 2012 Freeze 2012-01-06 2012-10-05 wgEncodeEM002393 2393 GSM929722 Ren LICR-m 10/13/10 Lane 4 cell 1x36 1 longPolyA Illumina_HiSeq_2000 F TopHat C57BL/6 wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Placenta Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Placenta Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6SigRep2 OFlact 8wk Sg 2 adult-8wks OlfactBulb RnaSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-20 wgEncodeEM002385 2385 GSM929712 Ren LICR-m 10/13/10 Lane 6 cell 1x36 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Olfactory Bulb Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Olfactory Bulb Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6SigRep1 OFlact 8wk Sg 1 adult-8wks OlfactBulb RnaSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-20 wgEncodeEM002385 2385 GSM929712 Ren LICR-m 10/13/10 Lane 6 cell 1x36 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Olfactory Bulb Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Olfactory Bulb Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6SigRep2 MEL Sg 2 immortalized MEL RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM002634 2634 GSM929704 Ren LICR-m 6/20/2011 Lane 2C cell 1x36 2 longPolyA Illumina_HiSeq_2000 M TopHat Unknown wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6SigRep2 Individual Signal Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male Unknown strain origin Tissue obtained from an individual Signal MEL Immortal cells RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6SigRep1 MEL Sg 1 immortalized MEL RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM002634 2634 GSM929704 Ren LICR-m 6/20/2011 Lane 2B cell 1x36 1 longPolyA Illumina_HiSeq_2000 M TopHat Unknown wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6SigRep1 Individual Signal Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male Unknown strain origin Tissue obtained from an individual Signal MEL Immortal cells RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6SigRep2 MEF 8wk Sg 2 adult-8wks MEF RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001708 1708 GSM929719 Ren LICR-m 03/15/10 Lane 6 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Mouse Embryonic Fibroblast Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal MEF Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6SigRep1 MEF 8wk Sg 1 adult-8wks MEF RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001708 1708 GSM929719 Ren LICR-m 03/15/10 Lane 5 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Mouse Embryonic Fibroblast Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal MEF Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6SigRep2 Lung 8wk Sg 2 adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001715 1715 GSM929710 Ren LICR-m 03/10/10 Lane 6 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Lung Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Lung Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6SigRep1 Lung 8wk Sg 1 adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001715 1715 GSM929710 Ren LICR-m 03/10/10 Lane 5 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Lung Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Lung Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6SigRep2 Liver E14.5 Sg 2 E14.5 Liver RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-04 wgEncodeEM002392 2392 GSM929721 Ren LICR-m 11/10/10 Lane 5 cell 1x36 2 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6SigRep2 Individual Signal Embryonic day 14.5 Liver Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Liver Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6SigRep1 Liver E14.5 Sg 1 E14.5 Liver RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-04 wgEncodeEM002392 2392 GSM929721 Ren LICR-m 11/10/10 Lane 5 cell 1x36 1 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6SigRep1 Individual Signal Embryonic day 14.5 Liver Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Liver Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6SigRep2 Liver 8wk Sg 2 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001714 1714 GSM929711 Ren LICR-m 03/02/10 Lane 4 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Liver Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Liver Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6SigRep1 Liver 8wk Sg 1 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001714 1714 GSM929711 Ren LICR-m 03/02/10 Lane 3 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Liver Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Liver Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6SigRep2 Limb E14.5 Sg 2 E14.5 Limb RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002387 2387 GSM929713 Ren LICR-m 11/10/10 Lane 5 cell 1x36 2 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6SigRep2 Individual Signal Embryonic day 14.5 Limb Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Limb Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6SigRep1 Limb E14.5 Sg 1 E14.5 Limb RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002387 2387 GSM929713 Ren LICR-m 11/10/10 Lane 5 cell 1x36 1 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6SigRep1 Individual Signal Embryonic day 14.5 Limb Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Limb Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6SigRep2 Kidney 8wk Sg 2 adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001713 1713 GSM929706 Ren LICR-m 03/15/10 Lane 4 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Kidney Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Kidney Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6SigRep1 Kidney 8wk Sg 1 adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001713 1713 GSM929706 Ren LICR-m 03/15/10 Lane 3 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Kidney Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Kidney Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6SigRep2 Heart E14.5 Sg 2 E14.5 Heart RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-04 wgEncodeEM002391 2391 GSM929724 Ren LICR-m 4/29/11 Lane 1 cell 1x36 2 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6SigRep2 Individual Signal Embryonic day 14.5 Heart Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Heart Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6SigRep1 Heart E14.5 Sg 1 E14.5 Heart RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-04 wgEncodeEM002391 2391 GSM929724 Ren LICR-m 4/29/11 Lane 1 cell 1x36 1 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6SigRep1 Individual Signal Embryonic day 14.5 Heart Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Heart Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6SigRep2 Heart 8wk Sg 2 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001712 1712 GSM929707 Ren LICR-m 03/10/10 Lane 2 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Heart Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Heart Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6SigRep1 Heart 8wk Sg 1 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001712 1712 GSM929707 Ren LICR-m 03/10/10 Lane 1 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Heart Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Heart Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6SigRep2 ES-Bruce4 E0 Sg 2 E0 ES-Bruce4 RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001707 1707 GSM929718 Ren LICR-m 10/13/10 Lane 4B cell 1x30 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6SigRep2 Individual Signal Embryonic day 0 (stem cell) mouse embryonic stem cells Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 30 nt read Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal ES-Bruce4 Embryonic day 0 RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6SigRep1 ES-Bruce4 E0 Sg 1 E0 ES-Bruce4 RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001707 1707 GSM929718 Ren LICR-m 10/13/10 Lane 4A cell 1x30 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6SigRep1 Individual Signal Embryonic day 0 (stem cell) mouse embryonic stem cells Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 30 nt read Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal ES-Bruce4 Embryonic day 0 RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6SigRep2 Cortex 8wk Sg 2 adult-8wks Cortex RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001711 1711 GSM929708 Ren LICR-m 03/15/10 Lane 2 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Cortex Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Cortex Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6SigRep1 Cortex 8wk Sg 1 adult-8wks Cortex RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001711 1711 GSM929708 Ren LICR-m 03/15/10 Lane 1 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Cortex Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Cortex Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6SigRep2 Crbellum 8wk Sg 2 adult-8wks Cerebellum RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001710 1710 GSM929709 Ren LICR-m 03/16/10 Lane 3 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Cerebellum Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Cerebellum Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6SigRep1 Crbellum 8wk Sg 1 adult-8wks Cerebellum RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001710 1710 GSM929709 Ren LICR-m 03/16/10 Lane 2 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Cerebellum Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Cerebellum Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6SigRep2 BMDM 8wk Sg 2 adult-8wks BMDM RnaSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002636 2636 GSM929705 Ren LICR-m 7/28/2011 Lane 2D cell 1x30 2 longPolyA Illumina_HiSeq_2000 F TopHat C57BL/6 wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Bone marrow derived macrophage Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 30 nt read Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal BMDM Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6SigRep1 BMDM 8wk Sg 1 adult-8wks BMDM RnaSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002636 2636 GSM929705 Ren LICR-m 7/28/2011 Lane 2C cell 1x30 1 longPolyA Illumina_HiSeq_2000 F TopHat C57BL/6 wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Bone marrow derived macrophage Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 30 nt read Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal BMDM Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6SigRep2 BM 8wk Sg 2 adult-8wks BoneMarrow RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001706 1706 GSM929717 Ren LICR-m 09/08/10 Lane 4H cell 1x30 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Bone Marrow Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 30 nt read Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Bone Marrow Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6SigRep1 BM 8wk Sg 1 adult-8wks BoneMarrow RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001706 1706 GSM929717 Ren LICR-m 09/08/10 Lane 4G cell 1x30 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6SigRep1 Individual Signal Adult 8 weeks Bone Marrow Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 30 nt read Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Bone Marrow Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6SigRep2 BAT 24wk Sg 2 adult-24wks BAT RnaSeq ENCODE Mar 2012 Freeze 2012-03-08 2012-12-08 wgEncodeEM002635 2635 GSM929703 Ren LICR-m 7/28/2011 Lane 3B cell 1x36 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6SigRep2 Individual Signal Adult 24 weeks Brown adipocytes tissue Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Brown Adipose Tissue Adult 24 weeks RNA-seq Signal Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6SigRep1 BAT 24wk Sg 1 adult-24wks BAT RnaSeq ENCODE Mar 2012 Freeze 2012-03-08 2012-12-08 wgEncodeEM002635 2635 GSM929703 Ren LICR-m 7/28/2011 Lane 3A cell 1x36 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6SigRep1 Individual Signal Adult 24 weeks Brown adipocytes tissue Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Brown Adipose Tissue Adult 24 weeks RNA-seq Signal Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqViewAlignments Alignments RNA-seq from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6AlnRep2 Brain E14.5 Al 2 E14.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002390 2390 Ren LICR-m 11/10/10 Lane 5 cell 1x36 2 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6AlnRep2 Individual Alignments Embryonic day 14.5 Whole Brain Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Whole Brain Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6AlnRep1 Brain E14.5 Al 1 E14.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002390 2390 Ren LICR-m 11/10/10 Lane 5 cell 1x36 1 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6AlnRep1 Individual Alignments Embryonic day 14.5 Whole Brain Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Whole Brain Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6AlnRep2 Thymus 8wk Al 2 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-20 wgEncodeEM002386 2386 Ren LICR-m 10/13/10 Lane 6 cell 1x36 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Thymus Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Thymus Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6AlnRep1 Thymus 8wk Al 1 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-20 wgEncodeEM002386 2386 Ren LICR-m 10/13/10 Lane 6 cell 1x36 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Thymus Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Thymus Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6AlnRep2 Testis 8wk Al 2 adult-8wks Testis RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002389 2389 Ren LICR-m 10/13/10 Lane 5 cell 1x36 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Testis Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Testis Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6AlnRep1 Testis 8wk Al 1 adult-8wks Testis RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002389 2389 Ren LICR-m 10/13/10 Lane 5 cell 1x36 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Testis Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Testis Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6AlnRep2 Spleen 8wk Al 2 adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001709 1709 Ren LICR-m 03/10/10 Lane 4 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Spleen Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Spleen Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6AlnRep1 Spleen 8wk Al 1 adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001709 1709 Ren LICR-m 03/10/10 Lane 3 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Spleen Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Spleen Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6AlnRep2 SmInt 8wk Al 2 adult-8wks SmIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002388 2388 Ren LICR-m 11/4/10 Lane 6 cell 1x36 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Small Intestine Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Small Intestine Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6AlnRep1 SmInt 8wk Al 1 adult-8wks SmIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002388 2388 Ren LICR-m 11/4/10 Lane 6 cell 1x36 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Small Intestine Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Small Intestine Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6AlnRep2 Placenta 8wk Al 2 adult-8wks Placenta RnaSeq ENCODE Mar 2012 Freeze 2012-01-06 2012-10-05 wgEncodeEM002393 2393 Ren LICR-m 10/13/10 Lane 4 cell 1x36 2 longPolyA Illumina_HiSeq_2000 F TopHat C57BL/6 wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Placenta Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Placenta Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6AlnRep1 Placenta 8wk Al 1 adult-8wks Placenta RnaSeq ENCODE Mar 2012 Freeze 2012-01-06 2012-10-05 wgEncodeEM002393 2393 Ren LICR-m 10/13/10 Lane 4 cell 1x36 1 longPolyA Illumina_HiSeq_2000 F TopHat C57BL/6 wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Placenta Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Placenta Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6AlnRep2 Olfact 8wk Al 2 adult-8wks OlfactBulb RnaSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-20 wgEncodeEM002385 2385 Ren LICR-m 10/13/10 Lane 6 cell 1x36 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Olfactory Bulb Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Olfactory Bulb Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6AlnRep1 Olfact 8wk Al 1 adult-8wks OlfactBulb RnaSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-20 wgEncodeEM002385 2385 Ren LICR-m 10/13/10 Lane 6 cell 1x36 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Olfactory Bulb Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Olfactory Bulb Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6AlnRep2 MEL Al 2 immortalized MEL RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM002634 2634 Ren LICR-m 6/20/2011 Lane 2C cell 1x36 2 longPolyA Illumina_HiSeq_2000 M TopHat Unknown wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6AlnRep2 Individual Alignments Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male Unknown strain origin Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch MEL Immortal cells RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6AlnRep1 MEL Al 1 immortalized MEL RnaSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM002634 2634 Ren LICR-m 6/20/2011 Lane 2B cell 1x36 1 longPolyA Illumina_HiSeq_2000 M TopHat Unknown wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6AlnRep1 Individual Alignments Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male Unknown strain origin Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch MEL Immortal cells RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6AlnRep2 MEF 8wk Al 2 adult-8wks MEF RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001708 1708 Ren LICR-m 03/15/10 Lane 6 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Mouse Embryonic Fibroblast Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch MEF Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6AlnRep1 MEF 8wk Al 1 adult-8wks MEF RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001708 1708 Ren LICR-m 03/15/10 Lane 5 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Mouse Embryonic Fibroblast Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch MEF Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6AlnRep2 Lung 8wk Al 2 adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001715 1715 Ren LICR-m 03/10/10 Lane 6 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Lung Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Lung Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6AlnRep1 Lung 8wk Al 1 adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001715 1715 Ren LICR-m 03/10/10 Lane 5 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Lung Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Lung Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6AlnRep2 Liver E14.5 Al 2 E14.5 Liver RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-04 wgEncodeEM002392 2392 Ren LICR-m 11/10/10 Lane 5 cell 1x36 2 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6AlnRep2 Individual Alignments Embryonic day 14.5 Liver Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Liver Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6AlnRep1 Liver E14.5 Al 1 E14.5 Liver RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-04 wgEncodeEM002392 2392 Ren LICR-m 11/10/10 Lane 5 cell 1x36 1 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6AlnRep1 Individual Alignments Embryonic day 14.5 Liver Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Liver Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6AlnRep2 Liver 8wk Al 2 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001714 1714 Ren LICR-m 03/02/10 Lane 4 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Liver Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Liver Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6AlnRep1 Liver 8wk Al 1 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001714 1714 Ren LICR-m 03/02/10 Lane 3 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Liver Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Liver Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6AlnRep2 Limb E14.5 Al 2 E14.5 Limb RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002387 2387 Ren LICR-m 11/10/10 Lane 5 cell 1x36 2 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6AlnRep2 Individual Alignments Embryonic day 14.5 Limb Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Limb Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6AlnRep1 Limb E14.5 Al 1 E14.5 Limb RnaSeq ENCODE Mar 2012 Freeze 2012-01-04 2012-10-03 wgEncodeEM002387 2387 Ren LICR-m 11/10/10 Lane 5 cell 1x36 1 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6AlnRep1 Individual Alignments Embryonic day 14.5 Limb Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Limb Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6AlnRep2 Kidney 8wk Al 2 adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001713 1713 Ren LICR-m 03/15/10 Lane 4 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Kidney Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Kidney Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6AlnRep1 Kidney 8wk Al 1 adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001713 1713 Ren LICR-m 03/15/10 Lane 3 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Kidney Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Kidney Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6AlnRep2 Heart E14.5 Al 2 E14.5 Heart RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-04 wgEncodeEM002391 2391 Ren LICR-m 4/29/11 Lane 1 cell 1x36 2 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6AlnRep2 Individual Alignments Embryonic day 14.5 Heart Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Heart Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6AlnRep1 Heart E14.5 Al 1 E14.5 Heart RnaSeq ENCODE Mar 2012 Freeze 2012-01-05 2012-10-04 wgEncodeEM002391 2391 Ren LICR-m 4/29/11 Lane 1 cell 1x36 1 longPolyA Illumina_HiSeq_2000 U TopHat C57BL/6 wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6AlnRep1 Individual Alignments Embryonic day 14.5 Heart Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Heart Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6AlnRep2 Heart 8wk Al 2 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001712 1712 Ren LICR-m 03/10/10 Lane 2 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Heart Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Heart Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6AlnRep1 Heart 8wk Al 1 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001712 1712 Ren LICR-m 03/10/10 Lane 1 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Heart Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Heart Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6AlnRep2 ES-Bruce4 E0 Al 2 E0 ES-Bruce4 RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001707 1707 Ren LICR-m 10/13/10 Lane 4B cell 1x30 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6AlnRep2 Individual Alignments Embryonic day 0 (stem cell) mouse embryonic stem cells Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 30 nt read Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch ES-Bruce4 Embryonic day 0 RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6AlnRep1 ES-Bruce4 E0 Al 1 E0 ES-Bruce4 RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001707 1707 Ren LICR-m 10/13/10 Lane 4A cell 1x30 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6AlnRep1 Individual Alignments Embryonic day 0 (stem cell) mouse embryonic stem cells Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 30 nt read Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch ES-Bruce4 Embryonic day 0 RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6AlnRep2 Cortex 8wk Al 2 adult-8wks Cortex RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001711 1711 Ren LICR-m 03/15/10 Lane 2 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Cortex Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Cortex Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6AlnRep1 Cortex 8wk Al 1 adult-8wks Cortex RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001711 1711 Ren LICR-m 03/15/10 Lane 1 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Cortex Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Cortex Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6AlnRep2 Crbellum 8wk Al 2 adult-8wks Cerebellum RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001710 1710 Ren LICR-m 03/16/10 Lane 3 cell 1x36 2 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Cerebellum Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Cerebellum Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6AlnRep1 Crbellum 8wk Al 1 adult-8wks Cerebellum RnaSeq ENCODE Mar 2012 Freeze 2011-05-12 2012-02-11 wgEncodeEM001710 1710 Ren LICR-m 03/16/10 Lane 2 cell 1x36 1 longPolyA Illumina_GA2 M TopHat C57BL/6 wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Cerebellum Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Cerebellum Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep2 BMDM 8wk Al 2 adult-8wks BMDM RnaSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002636 2636 Ren LICR-m 7/28/2011 Lane 2D cell 1x30 2 longPolyA Illumina_HiSeq_2000 F TopHat C57BL/6 wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Bone marrow derived macrophage Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 30 nt read Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch BMDM Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1 BMDM 8wk Al 1 adult-8wks BMDM RnaSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002636 2636 Ren LICR-m 7/28/2011 Lane 2C cell 1x30 1 longPolyA Illumina_HiSeq_2000 F TopHat C57BL/6 wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Bone marrow derived macrophage Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 30 nt read Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch BMDM Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6AlnRep2 BM 8wk Al 2 adult-8wks BoneMarrow RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001706 1706 Ren LICR-m 09/08/10 Lane 4H cell 1x30 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Bone Marrow Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 30 nt read Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Bone Marrow Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6AlnRep1 BM 8wk Al 1 adult-8wks BoneMarrow RnaSeq ENCODE Mar 2012 Freeze 2011-05-11 2012-02-11 wgEncodeEM001706 1706 Ren LICR-m 09/08/10 Lane 4G cell 1x30 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6AlnRep1 Individual Alignments Adult 8 weeks Bone Marrow Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 30 nt read Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Bone Marrow Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6AlnRep2 BAT 24wk Al 2 adult-24wks BAT RnaSeq ENCODE Mar 2012 Freeze 2012-03-08 2012-12-08 wgEncodeEM002635 2635 Ren LICR-m 7/28/2011 Lane 3B cell 1x36 2 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6AlnRep2 Individual Alignments Adult 24 weeks Brown adipocytes tissue Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Brown Adipose Tissue Adult 24 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6AlnRep1 BAT 24wk Al 1 adult-24wks BAT RnaSeq ENCODE Mar 2012 Freeze 2012-03-08 2012-12-08 wgEncodeEM002635 2635 Ren LICR-m 7/28/2011 Lane 3A cell 1x36 1 longPolyA Illumina_HiSeq_2000 M TopHat C57BL/6 wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6AlnRep1 Individual Alignments Adult 24 weeks Brown adipocytes tissue Sequencing analysis of RNA expression Ren Ren - Ludwig Institue for Cancer Research Whole cell Single 36 nt reads Poly(A)+ RNA longer than 200 nt Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Brown Adipose Tissue Adult 24 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbs LICR TFBS GSE36027 Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR Expression and Regulation Description This track shows a comprehensive survey of cis-regulatory elements in the mouse genome by using ChIP-seq &#40;Robertson et al., 2007&#41; to identify transcription factor binding sites (TFBS) and chromatin modification profiles in various mouse &#40;C57BL/6&#41; tissues, primary cells, and cell lines. The Ren lab examined RNA polymerase II &#40;PolII&#41;, co-activator protein p300, the insulator protein CTCF, and the following chromatin modification marks: H3K4me3 and H3K4me1, H3K27ac, H3K36me3, H3K9me3, and H3K27me3 due to their demonstrated utilities in identifying promoters, enhancers, insulator elements, actively transcribed gene bodies, and silent chromatin regions &#40;Barski et al., 2007; Bernstein et al., 2006; Blow et al., 2010; Creyghton et al., 2010; Francis et al., 2004; Hawkins et al., 2011; Heintzman et al., 2009; Kim et al., 2007; Kim et al., 2005; Krogan et al., 2003; Li et al., 2002; Peters et al., 2001; Rada-Iglesias et al., 2011; Schotta et al., 2002; Visel et al., 2009&#41;. Enrichment of PolII signals is a strong indicator of an active promoter and the presence of p300 outside of promoter regions has been used as a mark for enhancers. CTCF binding sites are considered as a mark for potential insulator elements. H3K4me3 is an active mark for promoters and H3K27ac is an active mark for both promoters and enhancers. In the absence of H3K4me3, H3K4me1 serves as an active mark for enhancers. H3K36me3 is normally found in actively transcribed gene bodies whereas both H3K9me3 and H3K27me3 are common repressive marks for transcriptionally silent chromatin regions. For each transcription factor or chromatin mark in each tissue, ChIP-seq was carried out with at least two biological replicates. Each experiment produced 20-30 million uniquely-mapped monoclonal tags. 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. This track contains the following views: Peaks Regions of signal enrichment based on processed data (normalized data from pooled replicates). Intensity is represented in grayscale; darker shading shows higher intensity (a solid vertical line in the peak region represents the point with the highest signal). 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. Additional views are available on the Downloads page. Methods Cells were grown according to the approved ENCODE cell culture protocols. Enrichment and Library Preparation Chromatin immunoprecipitation was performed according to the Ren Lab ChIP Protocol. Library construction was performed according to the Ren Lab Library Protocol. Sequencing and Analysis Samples were sequenced on Illumina Genome Analyzer II, Genome Analyzer IIx and HiSeq 2000 platforms for 36 cycles. Image analysis, base calling and alignment to the mouse genome version NCBI37/mm9 were performed using Illumina&#39;s RTA and Genome Analyzer Pipeline software. Alignment to the mouse genome was performed using ELAND or Bowtie (Langmead et al., 2009) with a seed length of 25 and allowing up to two mismatches. Only the sequences that mapped to one location were used for further analysis. Of those sequences, clonal reads, defined as having the same start position on the same strand, were discarded. BED and wig files were created using custom perl scripts. Release Notes This is Release 3 (August 2012). It contains a total of 58 ChIP-seq experiments on transcription factor binding. In this release, four controls (inputs) were dropped because they did not have accompanying TFBS experiments. An error surrounding the metadata designation of replicates of the fastq and alignment files of Kidney PolII datasets has been fixed. Credits These data were generated and analyzed in Bing Ren&#39;s laboratory at the Ludwig Institute for Cancer Research (LICR). Contact: Yin Shen References Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell. 2007 May 18;129(4):823-37. 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. Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet. 2010 Sep;42(9):806-10. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6. Francis NJ, Kingston RE, Woodcock CL. Chromatin compaction by a polycomb group protein complex. Science. 2004 Nov 26;306(5701):1574-7. Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z et al. Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Res. 2011 Oct;21(10):1393-409. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 2009 May 7;459(7243):108-12. Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell. 2007 Mar 23;128(6):1231-45. Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM et al. Direct isolation and identification of promoters in the human genome. Genome Res. 2005 Jun;15(6):830-9. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C et al. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol. 2003 Jun;23(12):4207-18. 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 J, Moazed D, Gygi SP. Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. J Biol Chem. 2002 Dec 20;277(51):49383-8. Peters AH, O'Carroll D, Scherthan H, Mechtler K, Sauer S, Sch&#246;fer C, Weipoltshammer K, Pagani M, Lachner M, Kohlmaier A et al. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell. 2001 Nov 2;107(3):323-37. Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 2011 Feb 10;470(7333):279-83. 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. Schotta G, Ebert A, Krauss V, Fischer A, Hoffmann J, Rea S, Jenuwein T, Dorn R, Reuter G. Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing. EMBO J. 2002 Mar 1;21(5):1121-31. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009 Feb 12;457(7231):854-8. 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. 
wgEncodeLicrTfbsViewSignal Signal Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsWbrainPol2UE14halfC57bl6StdSig Brain 14.5 Pol2 E14.5 Pol2 WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002596 2596 GSM918706 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrTfbsWbrainPol2UE14halfC57bl6StdSig Signal Embryonic day 14.5 RNA Polymerase II Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain Embryonic day 14.5 Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsWbrainInputUE14halfC57bl6StdSig Brain 14.5 Input E14.5 Input WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002494 2494 GSM918752 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input U Custom Scripts C57BL/6 wgEncodeLicrTfbsWbrainInputUE14halfC57bl6StdSig Signal Embryonic day 14.5 Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain Embryonic day 14.5 Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsWbrainCtcfUE14halfC57bl6StdSig Brain 14.5 CTCF E14.5 CTCF WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002595 2595 GSM918730 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrTfbsWbrainCtcfUE14halfC57bl6StdSig Signal Embryonic day 14.5 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain Embryonic day 14.5 CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsThymusPol2MAdult8wksC57bl6StdSig Thymus 8w Pol2 adult-8wks Pol2 Thymus std ChipSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002588 2588 GSM918742 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsThymusPol2MAdult8wksC57bl6StdSig Signal Adult 8 weeks RNA Polymerase II Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Thymus Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsThymusInputMAdult8wksC57bl6StdSig Thymus 8w Input adult-8wks Input Thymus std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002477 2477 GSM918705 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsThymusInputMAdult8wksC57bl6StdSig Signal Adult 8 weeks Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Thymus Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsThymusCtcfMAdult8wksC57bl6StdSig Thymus 8w CTCF adult-8wks CTCF Thymus std ChipSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002587 2587 GSM918734 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsThymusCtcfMAdult8wksC57bl6StdSig Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Thymus Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsTestisPol2MAdult8wksC57bl6StdSig Testis 8w Pol2 adult-8wks Pol2 Testis std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002594 2594 GSM918704 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsTestisPol2MAdult8wksC57bl6StdSig Signal Adult 8 weeks RNA Polymerase II Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Testis Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsTestisInputMAdult8wksC57bl6StdSig Testis 8w Input adult-8wks Input Testis std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002490 2490 GSM918751 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsTestisInputMAdult8wksC57bl6StdSig Signal Adult 8 weeks Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Testis Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsTestisCtcfMAdult8wksC57bl6StdSig Testis 8w CTCF adult-8wks CTCF Testis std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002593 2593 GSM918711 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsTestisCtcfMAdult8wksC57bl6StdSig Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Testis Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsSpleenPol2MAdult8wksC57bl6StdSig Spleen 8w Pol2 adult-8wks Pol2 Spleen std ChipSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001701 1701 GSM918746 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsSpleenPol2MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks RNA Polymerase II Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Spleen Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsSpleenInputMAdult8wksC57bl6StdSig Spleen 8w Input adult-8wks Input Spleen std ChipSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001459 1459 GSM918763 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsSpleenInputMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Spleen Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsSpleenCtcfMAdult8wksC57bl6StdSig Spleen 8w CTCF adult-8wks CTCF Spleen std ChipSeq ENCODE Mar 2012 Freeze 2011-04-29 2012-01-28 wgEncodeEM001700 1700 GSM918745 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsSpleenCtcfMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Spleen Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsSmintPol2MAdult8wksC57bl6StdSig SmInt 8w Pol2 adult-8wks Pol2 SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002592 2592 GSM918710 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsSmintPol2MAdult8wksC57bl6StdSig Signal Adult 8 weeks RNA Polymerase II Small Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Small Intestine Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsSmintInputMAdult8wksC57bl6StdSig SmInt 8w Input adult-8wks Input SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002486 2486 GSM918717 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsSmintInputMAdult8wksC57bl6StdSig Signal Adult 8 weeks Small Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Small Intestine Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsSmintCtcfMAdult8wksC57bl6StdSig SmInt 8w CTCF adult-8wks CTCF SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002591 2591 GSM918709 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsSmintCtcfMAdult8wksC57bl6StdSig Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding 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 Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Small Intestine Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsOlfactPol2MAdult8wksC57bl6StdSig Olfact 8w Pol2 adult-8wks Pol2 OlfactBulb std ChipSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002586 2586 GSM918735 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsOlfactPol2MAdult8wksC57bl6StdSig Signal Adult 8 weeks RNA Polymerase II Olfactory Bulb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Olfactory Bulb Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsOlfactInputMAdult8wksC57bl6StdSig Olfact 8w Input adult-8wks Input OlfactBulb std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002473 2473 GSM918714 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsOlfactInputMAdult8wksC57bl6StdSig Signal Adult 8 weeks Olfactory Bulb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Olfactory Bulb Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsOlfactCtcfMAdult8wksC57bl6StdSig Olfact 8w CTCF adult-8wks CTCF OlfactBulb std ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEM002585 2585 GSM918736 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsOlfactCtcfMAdult8wksC57bl6StdSig Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Olfactory Bulb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal Olfactory Bulb Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsMelPol2MImmortalC57bl6StdSig MEL Immort Pol2 immortalized Pol2 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM002662 2662 GSM918707 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts Unknown wgEncodeLicrTfbsMelPol2MImmortalC57bl6StdSig Signal Immortal cells RNA Polymerase II Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Signal MEL Immortal cells Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsMelInputMImmortalC57bl6StdSig MEL Immort Input immortalized Input MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM002652 2652 GSM918712 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 input M Custom Scripts Unknown wgEncodeLicrTfbsMelInputMImmortalC57bl6StdSig Signal Immortal cells Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Signal MEL Immortal cells Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsMelCtcfMImmortalC57bl6StdSig MEL Immort CTCF immortalized CTCF MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM002661 2661 GSM918744 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp M Custom Scripts Unknown wgEncodeLicrTfbsMelCtcfMImmortalC57bl6StdSig Signal Immortal cells CTCF zinc finger transcription factor. A sequence specific DNA binding 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Signal MEL Immortal cells CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsMefPol2MAdult8wksC57bl6StdSig MEF 8w Pol2 adult-8wks Pol2 MEF std ChipSeq ENCODE Mar 2012 Freeze 2011-04-29 2012-01-28 wgEncodeEM001699 1699 GSM918761 Ren LICR-m Pooled & normalized Illumina_GA2x exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsMefPol2MAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks RNA Polymerase II Mouse Embryonic Fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer IIx Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal MEF Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsMefInputMAdult8wksC57bl6StdSig MEF 8w Input adult-8wks Input MEF std ChipSeq ENCODE Mar 2012 Freeze 2011-04-29 2012-01-28 wgEncodeEM001456 1456 GSM918740 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsMefInputMAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks Mouse Embryonic Fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal MEF Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsMefCtcfMAdult8wksC57bl6StdSig MEF 8w CTCF adult-8wks CTCF MEF std ChipSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEM001698 1698 GSM918743 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsMefCtcfMAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Mouse Embryonic Fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal MEF Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLungPol2MAdult8wksC57bl6StdSig Lung 8w Pol2 adult-8wks Pol2 Lung std ChipSeq ENCODE Mar 2012 Freeze 2011-04-15 2012-01-14 wgEncodeEM001695 1695 GSM918724 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsLungPol2MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks RNA Polymerase II Lung Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Lung Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLungInputMAdult8wksC57bl6StdSig Lung 8w Input adult-8wks Input Lung std ChipSeq ENCODE Mar 2012 Freeze 2011-04-25 2012-01-25 wgEncodeEM001453 1453 GSM918739 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsLungInputMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Lung Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Lung Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLungCtcfMAdult8wksC57bl6StdSig Lung 8w CTCF adult-8wks CTCF Lung std ChipSeq ENCODE Mar 2012 Freeze 2011-04-25 2012-01-25 wgEncodeEM001697 1697 GSM918722 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsLungCtcfMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding 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 Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Lung Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLiverPol2MAdult8wksC57bl6StdSig Liver 8w Pol2 adult-8wks Pol2 Liver std ChipSeq ENCODE Mar 2012 Freeze 2011-04-13 2012-01-13 wgEncodeEM001693 1693 GSM918738 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsLiverPol2MAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks RNA Polymerase II Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Liver Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLiverInputUE14halfC57bl6StdSig Liver 14.5 Input E14.5 Input Liver std ChipSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-13 wgEncodeEM002570 2570 GSM918753 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input U Custom Scripts C57BL/6 wgEncodeLicrTfbsLiverInputUE14halfC57bl6StdSig Signal Embryonic day 14.5 Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Liver Embryonic day 14.5 Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLiverInputMAdult8wksC57bl6StdSig Liver 8w Input adult-8wks Input Liver std ChipSeq ENCODE Mar 2012 Freeze 2011-04-25 2012-01-25 wgEncodeEM001452 1452 GSM918718 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsLiverInputMAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Liver Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLiverCtcfMAdult8wksC57bl6StdSig Liver 8w CTCF adult-8wks CTCF Liver std ChipSeq ENCODE Mar 2012 Freeze 2011-04-25 2012-01-25 wgEncodeEM001696 1696 GSM918715 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsLiverCtcfMAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Liver Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdSig Limb 14.5 Pol2 E14.5 Pol2 Limb std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-23 wgEncodeEM002590 2590 GSM918708 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U Custom Scripts C57BL/6 wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdSig Signal Embryonic day 14.5 RNA Polymerase II Limb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Limb Embryonic day 14.5 Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLimbInputUE14halfC57bl6StdSig Limb 14.5 Input E14.5 Input Limb std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002482 2482 GSM918719 Ren LICR-m Pooled & filtered Illumina_GA2 input U Custom Scripts C57BL/6 wgEncodeLicrTfbsLimbInputUE14halfC57bl6StdSig Signal Embryonic day 14.5 Limb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Limb Embryonic day 14.5 Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdSig Limb 14.5 CTCF E14.5 CTCF Limb std ChipSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-23 wgEncodeEM002589 2589 GSM918741 Ren LICR-m Pooled & filtered Illumina_GA2 exp U Custom Scripts C57BL/6 wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdSig Signal Embryonic day 14.5 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Limb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Limb Embryonic day 14.5 CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdSig Kidney 8w Pol2 adult-8wks Pol2 Kidney std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2010-11-18 2011-08-18 wgEncodeEM001686 1686 GSM918758 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks RNA Polymerase II Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Kidney Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsKidneyInputMAdult8wksC57bl6StdSig Kidney 8w Input adult-8wks Input Kidney std ChipSeq ENCODE Mar 2012 Freeze 2011-04-24 2012-01-24 wgEncodeEM001451 1451 GSM918716 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsKidneyInputMAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Kidney Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsKidneyCtcfMAdult8wksC57bl6StdSig Kidney 8w CTCF adult-8wks CTCF Kidney std ChipSeq ENCODE Mar 2012 Freeze 2011-04-07 2010-11-18 2011-08-18 wgEncodeEM001685 1685 GSM918731 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsKidneyCtcfMAdult8wksC57bl6StdSig Individual Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Kidney Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsHeartPol2MAdult8wksC57bl6StdSig Heart 8w Pol2 adult-8wks Pol2 Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-04-14 2012-01-13 wgEncodeEM001694 1694 GSM918723 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsHeartPol2MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks RNA Polymerase II Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Heart Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsHeartP300MAdult8wksC57bl6StdSig Heart 8w p300 adult-8wks p300 Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-05-03 2012-02-03 wgEncodeEM001702 1702 GSM918747 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsHeartP300MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks EP300(c-20) Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Heart Adult 8 weeks p300 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsHeartInputUE14halfC57bl6StdSig Heart 14.5 Input E14.5 Input Heart std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002506 2506 GSM918729 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 input U Custom Scripts C57BL/6 wgEncodeLicrTfbsHeartInputUE14halfC57bl6StdSig Signal Embryonic day 14.5 Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Signal Heart Embryonic day 14.5 Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsHeartInputMAdult8wksC57bl6StdSig Heart 8w Input adult-8wks Input Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-04-25 2012-01-24 wgEncodeEM001450 1450 GSM918755 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsHeartInputMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Heart Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsHeartCtcfMAdult8wksC57bl6StdSig Heart 8w CTCF adult-8wks CTCF Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2010-11-01 2011-08-01 wgEncodeEM001684 1684 GSM918756 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsHeartCtcfMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Heart Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsEsb4Pol2ME0C57bl6StdSig ES-B4 E0 Pol2 E0 Pol2 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001704 1704 GSM918749 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsEsb4Pol2ME0C57bl6StdSig Individual Signal Embryonic day 0 (stem cell) RNA Polymerase II mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal ES-Bruce4 Embryonic day 0 Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsEsb4P300ME0C57bl6StdSig ES-B4 E0 p300 E0 p300 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-05 wgEncodeEM001705 1705 GSM918750 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsEsb4P300ME0C57bl6StdSig Individual Signal Embryonic day 0 (stem cell) EP300(c-20) mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal ES-Bruce4 Embryonic day 0 p300 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsEsb4InputME0C57bl6StdSig ES-B4 E0 Input E0 Input ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-05 wgEncodeEM001683 1683 GSM918754 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsEsb4InputME0C57bl6StdSig Individual Signal Embryonic day 0 (stem cell) mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal ES-Bruce4 Embryonic day 0 Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsEsb4CtcfME0C57bl6StdSig ES-B4 E0 CTCF E0 CTCF ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001703 1703 GSM918748 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsEsb4CtcfME0C57bl6StdSig Individual Signal Embryonic day 0 (stem cell) CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal ES-Bruce4 Embryonic day 0 CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsCortexPol2MAdult8wksC57bl6StdSig Cortex 8w Pol2 adult-8wks Pol2 Cortex std ChipSeq ENCODE Mar 2012 Freeze 2011-01-20 2011-10-19 wgEncodeEM001691 1691 GSM918728 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsCortexPol2MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks RNA Polymerase II Cortex Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cortex Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsCortexInputMAdult8wksC57bl6StdSig Cortex 8w Input adult-8wks Input Cortex std ChipSeq ENCODE Mar 2012 Freeze 2011-01-20 2011-10-19 wgEncodeEM001449 1449 GSM918732 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsCortexInputMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Cortex Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cortex Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsCortexCtcfMAdult8wksC57bl6StdSig Cortex 8w CTCF adult-8wks CTCF Cortex std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001690 1690 GSM918727 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsCortexCtcfMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Cortex Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cortex Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsCbellumPol2MAdult8wksC57bl6StdSig Cb 8w Pol2 adult-8wks Pol2 Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-12-07 wgEncodeEM001692 1692 GSM918725 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsCbellumPol2MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks RNA Polymerase II Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cerebellum Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsCbellumInputMAdult8wksC57bl6StdSig Cb 8w Input adult-8wks Input Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2011-04-22 2010-10-15 2011-07-15 wgEncodeEM001448 1448 GSM918733 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsCbellumInputMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cerebellum Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdSig Cb 8w CTCF adult-8wks CTCF Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001689 1689 GSM918759 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cerebellum Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsBmdmPol2FAdult8wksC57bl6StdSig BMDM 8w Pol2 adult-8wks Pol2 BMDM std ChipSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002664 2664 GSM918720 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrTfbsBmdmPol2FAdult8wksC57bl6StdSig Signal Adult 8 weeks RNA Polymerase II Bone marrow derived macrophage Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal BMDM Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsBmdmInputFAdult8wksC57bl6StdSig BMDM 8w Input adult-8wks Input BMDM std ChipSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002660 2660 GSM918737 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 input F Custom Scripts C57BL/6 wgEncodeLicrTfbsBmdmInputFAdult8wksC57bl6StdSig Signal Adult 8 weeks Bone marrow derived macrophage Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal BMDM Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsBmdmCtcfFAdult8wksC57bl6StdSig BMDM 8w CTCF adult-8wks CTCF BMDM std ChipSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002663 2663 GSM918726 Ren LICR-m Pooled & normalized Illumina_HiSeq_2000 exp F Custom Scripts C57BL/6 wgEncodeLicrTfbsBmdmCtcfFAdult8wksC57bl6StdSig Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Bone marrow derived macrophage Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Signal BMDM Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdSig BM 8w Pol2 adult-8wks Pol2 BoneMarrow std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001688 1688 GSM918760 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom Scripts C57BL/6 wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks RNA Polymerase II Bone Marrow Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Bone Marrow Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsBmarrowInputMAdult8wksC57bl6StdSig BM 8w Input adult-8wks Input BoneMarrow std ChipSeq ENCODE Mar 2012 Freeze 2011-04-22 2012-01-21 wgEncodeEM001447 1447 GSM918721 Ren LICR-m Pooled & normalized Illumina_GA2 input M Custom Scripts C57BL/6 wgEncodeLicrTfbsBmarrowInputMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks Bone Marrow Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Bone Marrow Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdSig BM 8w CTCF adult-8wks CTCF BoneMarrow std ChipSeq ENCODE Mar 2012 Freeze 2011-01-05 2011-10-05 wgEncodeEM001687 1687 GSM918757 Ren LICR-m Pooled & normalized Illumina_GA2 exp M Custom scripts C57BL/6 wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdSig Pooled Signal Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Bone Marrow Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Bone Marrow Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsViewPeaks Peaks Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsWbrainPol2UE14halfC57bl6StdPk Brain 14.5 Pol2 E14.5 Pol2 WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002596 2596 GSM918706 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrTfbsWbrainPol2UE14halfC57bl6StdPk Peaks Embryonic day 14.5 RNA Polymerase II Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Whole Brain Embryonic day 14.5 Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsWbrainCtcfUE14halfC57bl6StdPk Brain 14.5 CTCF E14.5 CTCF WholeBrain std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002595 2595 GSM918730 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrTfbsWbrainCtcfUE14halfC57bl6StdPk Peaks Embryonic day 14.5 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Whole Brain Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Whole Brain Embryonic day 14.5 CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsThymusPol2MAdult8wksC57bl6StdPk Thymus 8w Pol2 adult-8wks Pol2 Thymus std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002588 2588 GSM918742 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrTfbsThymusPol2MAdult8wksC57bl6StdPk Peaks Adult 8 weeks RNA Polymerase II Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Thymus Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsThymusCtcfMAdult8wksC57bl6StdPk Thymus 8w CTCF adult-8wks CTCF Thymus std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002587 2587 GSM918734 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrTfbsThymusCtcfMAdult8wksC57bl6StdPk Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Thymus Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Thymus Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsTestisPol2MAdult8wksC57bl6StdPk Testis 8w Pol2 adult-8wks Pol2 Testis std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002594 2594 GSM918704 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrTfbsTestisPol2MAdult8wksC57bl6StdPk Peaks Adult 8 weeks RNA Polymerase II Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Testis Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsTestisCtcfMAdult8wksC57bl6StdPk Testis 8w CTCF adult-8wks CTCF Testis std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002593 2593 GSM918711 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrTfbsTestisCtcfMAdult8wksC57bl6StdPk Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Testis Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Testis Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsSpleenPol2MAdult8wksC57bl6StdPk Spleen 8w Pol2 adult-8wks Pol2 Spleen std ChipSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001701 1701 GSM918746 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsSpleenPol2MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks RNA Polymerase II Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Spleen Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsSpleenCtcfMAdult8wksC57bl6StdPk Spleen 8w CTCF adult-8wks CTCF Spleen std ChipSeq ENCODE Mar 2012 Freeze 2011-04-29 2012-01-28 wgEncodeEM001700 1700 GSM918745 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrTfbsSpleenCtcfMAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Spleen Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Spleen Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsSmintPol2MAdult8wksC57bl6StdPk SI 8w Pol2 adult-8wks Pol2 SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002592 2592 GSM918710 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrTfbsSmintPol2MAdult8wksC57bl6StdPk Peaks Adult 8 weeks RNA Polymerase II Small Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Small Intestine Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsSmintCtcfMAdult8wksC57bl6StdPk SmInt 8w CTCF adult-8wks CTCF SmIntestine std ChipSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM002591 2591 GSM918709 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrTfbsSmintCtcfMAdult8wksC57bl6StdPk Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding 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 Intestine Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Small Intestine Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsOlfactPol2MAdult8wksC57bl6StdPk Olfact 8w Pol2 adult-8wks Pol2 OlfactBulb std ChipSeq ENCODE Mar 2012 Freeze 2012-02-16 2012-11-15 wgEncodeEM002586 2586 GSM918735 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrTfbsOlfactPol2MAdult8wksC57bl6StdPk Peaks Adult 8 weeks RNA Polymerase II Olfactory Bulb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Olfactory Bulb Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsOlfactCtcfMAdult8wksC57bl6StdPk Olfact 8w CTCF adult-8wks CTCF OlfactBulb std ChipSeq ENCODE Mar 2012 Freeze 2011-12-21 2012-09-21 wgEncodeEM002585 2585 GSM918736 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS C57BL/6 wgEncodeLicrTfbsOlfactCtcfMAdult8wksC57bl6StdPk Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Olfactory Bulb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Olfactory Bulb Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsMelPol2MImmortalC57bl6StdPk MEL Immort Pol2 immortalized Pol2 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM002662 2662 GSM918707 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS Unknown wgEncodeLicrTfbsMelPol2MImmortalC57bl6StdPk Peaks Immortal cells RNA Polymerase II Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Regions of enriched signal in experiment MEL Immortal cells Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsMelCtcfMImmortalC57bl6StdPk MEL Immort CTCF immortalized CTCF MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM002661 2661 GSM918744 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp M MACS Unknown wgEncodeLicrTfbsMelCtcfMImmortalC57bl6StdPk Peaks Immortal cells CTCF zinc finger transcription factor. A sequence specific DNA binding 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Male Unknown strain origin Regions of enriched signal in experiment MEL Immortal cells CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsMefPol2MAdult8wksC57bl6StdPk MEF 8w Pol2 adult-8wks Pol2 MEF std ChipSeq ENCODE Mar 2012 Freeze 2011-04-29 2012-01-28 wgEncodeEM001699 1699 GSM918761 Ren LICR-m Pooled & filtered Illumina_GA2x exp M MACS C57BL/6 wgEncodeLicrTfbsMefPol2MAdult8wksC57bl6StdPk Individual Peaks Adult 8 weeks RNA Polymerase II Mouse Embryonic Fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer IIx Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment MEF Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsMefCtcfMAdult8wksC57bl6StdPk MEF 8w CTCF adult-8wks CTCF MEF std ChipSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEM001698 1698 GSM918743 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsMefCtcfMAdult8wksC57bl6StdPk Individual Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Mouse Embryonic Fibroblast Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment MEF Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLungPol2MAdult8wksC57bl6StdPk Lung 8w Pol2 adult-8wks Pol2 Lung std ChipSeq ENCODE Mar 2012 Freeze 2011-04-15 2012-01-14 wgEncodeEM001695 1695 GSM918724 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsLungPol2MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks RNA Polymerase II Lung Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Lung Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLungCtcfMAdult8wksC57bl6StdPk Lung 8w CTCF adult-8wks CTCF Lung std ChipSeq ENCODE Mar 2012 Freeze 2011-04-25 2012-01-25 wgEncodeEM001697 1697 GSM918722 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsLungCtcfMAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding 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 Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Lung Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLiverPol2MAdult8wksC57bl6StdPk Liver 8w Pol2 adult-8wks Pol2 Liver std ChipSeq ENCODE Mar 2012 Freeze 2011-04-13 2012-01-13 wgEncodeEM001693 1693 GSM918738 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsLiverPol2MAdult8wksC57bl6StdPk Individual Peaks Adult 8 weeks RNA Polymerase II Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Liver Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLiverCtcfMAdult8wksC57bl6StdPk Liver 8w CTCF adult-8wks CTCF Liver std ChipSeq ENCODE Mar 2012 Freeze 2011-04-25 2012-01-25 wgEncodeEM001696 1696 GSM918715 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsLiverCtcfMAdult8wksC57bl6StdPk Individual Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Liver Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Liver Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdPk Limb 14.5 Pol2 E14.5 Pol2 Limb std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002590 2590 GSM918708 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp U MACS C57BL/6 wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdPk Peaks Embryonic day 14.5 RNA Polymerase II Limb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Limb Embryonic day 14.5 Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdPk Limb 14.5 CTCF E14.5 CTCF Limb std ChipSeq ENCODE Mar 2012 Freeze 2012-02-14 2012-11-14 wgEncodeEM002589 2589 GSM918741 Ren LICR-m Pooled & filtered Illumina_GA2 exp U MACS C57BL/6 wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdPk Peaks Embryonic day 14.5 CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Limb Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Unknown C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Limb Embryonic day 14.5 CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdPk Kidney 8w Pol2 adult-8wks Pol2 Kidney std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2010-11-18 2011-08-18 wgEncodeEM001686 1686 GSM918758 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdPk Individual Peaks Adult 8 weeks RNA Polymerase II Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Kidney Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsKidneyCtcfMAdult8wksC57bl6StdPk Kidney 8w CTCF adult-8wks CTCF Kidney std ChipSeq ENCODE Mar 2012 Freeze 2011-04-07 2010-11-18 2011-08-18 wgEncodeEM001685 1685 GSM918731 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsKidneyCtcfMAdult8wksC57bl6StdPk Individual Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Kidney Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Kidney Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsHeartPol2MAdult8wksC57bl6StdPk Heart 8w Pol2 adult-8wks Pol2 Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-04-14 2012-01-13 wgEncodeEM001694 1694 GSM918723 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsHeartPol2MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks RNA Polymerase II Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Heart Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsHeartP300MAdult8wksC57bl6StdPk Heart 8w p300 adult-8wks p300 Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-05-03 2012-02-03 wgEncodeEM001702 1702 GSM918747 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsHeartP300MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks EP300(c-20) Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Heart Adult 8 weeks p300 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsHeartCtcfMAdult8wksC57bl6StdPk Heart 8w CTCF adult-8wks CTCF Heart std ChipSeq ENCODE Mar 2012 Freeze 2011-04-12 2010-11-01 2011-08-01 wgEncodeEM001684 1684 GSM918756 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsHeartCtcfMAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Heart Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Heart Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsEsb4Pol2ME0C57bl6StdPk ES-B4 E0 Pol2 E0 Pol2 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001704 1704 GSM918749 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsEsb4Pol2ME0C57bl6StdPk Individual Peaks Embryonic day 0 (stem cell) RNA Polymerase II mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment ES-Bruce4 Embryonic day 0 Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsEsb4P300ME0C57bl6StdPk ES-B4 E0 p300 E0 p300 ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-05 wgEncodeEM001705 1705 GSM918750 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsEsb4P300ME0C57bl6StdPk Individual Peaks Embryonic day 0 (stem cell) EP300(c-20) mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment ES-Bruce4 Embryonic day 0 p300 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsEsb4CtcfME0C57bl6StdPk ES-B4 E0 CTCF E0 CTCF ES-Bruce4 std ChipSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001703 1703 GSM918748 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsEsb4CtcfME0C57bl6StdPk Individual Peaks Embryonic day 0 (stem cell) CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. mouse embryonic stem cells Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment ES-Bruce4 Embryonic day 0 CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsCortexPol2MAdult8wksC57bl6StdPk Cortex 8w Pol2 adult-8wks Pol2 Cortex std ChipSeq ENCODE Mar 2012 Freeze 2011-01-20 2011-10-19 wgEncodeEM001691 1691 GSM918728 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsCortexPol2MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks RNA Polymerase II Cortex Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Cortex Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsCortexCtcfMAdult8wksC57bl6StdPk Cortex 8w CTCF adult-8wks CTCF Cortex std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001690 1690 GSM918727 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsCortexCtcfMAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Cortex Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Cortex Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsCbellumPol2MAdult8wksC57bl6StdPk Cb 8w Pol2 adult-8wks Pol2 Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2011-03-07 2011-12-07 wgEncodeEM001692 1692 GSM918725 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsCbellumPol2MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks RNA Polymerase II Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Cerebellum Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdPk Cb 8w CTCF adult-8wks CTCF Cerebellum std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001689 1689 GSM918759 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Cerebellum Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Cerebellum Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsBmdmPol2FAdult8wksC57bl6StdPk BMDM 8w Pol2 adult-8wks Pol2 BMDM std ChipSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002664 2664 GSM918720 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrTfbsBmdmPol2FAdult8wksC57bl6StdPk Peaks Adult 8 weeks RNA Polymerase II Bone marrow derived macrophage Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment BMDM Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsBmdmCtcfFAdult8wksC57bl6StdPk BMDM 8w CTCF adult-8wks CTCF BMDM std ChipSeq ENCODE Mar 2012 Freeze 2012-03-10 2012-12-09 wgEncodeEM002663 2663 GSM918726 Ren LICR-m Pooled & filtered Illumina_HiSeq_2000 exp F MACS C57BL/6 wgEncodeLicrTfbsBmdmCtcfFAdult8wksC57bl6StdPk Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Bone marrow derived macrophage Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina HiSeq 2000 Female C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment BMDM Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdPk BM 8w Pol2 adult-8wks Pol2 BoneMarrow std ChipSeq ENCODE Mar 2012 Freeze 2011-01-19 2011-10-19 wgEncodeEM001688 1688 GSM918760 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks RNA Polymerase II Bone Marrow Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Bone Marrow Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdPk BM 8w CTCF adult-8wks CTCF BoneMarrow std ChipSeq ENCODE Mar 2012 Freeze 2011-01-05 2011-10-05 wgEncodeEM001687 1687 GSM918757 Ren LICR-m Pooled & filtered Illumina_GA2 exp M MACS C57BL/6 wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdPk Pooled Peaks Adult 8 weeks CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Bone Marrow Standard input signal for most experiments. Chromatin IP Sequencing Ren Ren - Ludwig Institue for Cancer Research Illumina Genome Analyzer II Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Bone Marrow Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR Expression and Regulation 
ctgPos Map Contigs Physical Map Contigs Mapping and Sequencing Description This track shows the locations of mouse contigs on the physical map. The underlying data are derived from NCBI information specific to this assembly. Although the NCBI data indicates the orientations of the contigs based on how they were assembled into the final sequence, all contigs in this track are oriented to the &quot;+&quot; strand. 
wgEncodeMapability Mappability Mappability or Uniqueness of Reference Genome from ENCODE Mapping and Sequencing Description These tracks display the level of sequence uniqueness of the reference mm9 genome. They were generated using different window sizes and high signal will be found in areas where the sequence is unique. Display Conventions and Configuration This track contains multiple subtracks representing different cell types that display individually on the browser. Instructions for configuring tracks with multiple subtracks are here. These tracks provide a measure of how often the sequence found at the particular location will align within the whole genome. Unlike measures of uniqueness, alignability will tolerate up to 2 mismatches. These tracks are in the form of signals ranging from 0 to 1 and have several configuration options. Methods The CRG Alignability tracks show how uniquely k-mer sequences align to a region of the genome. By using the GEM mapper aligner, where up to two mismatches were allowed, the method is equivalent to mapping sliding windows of k-mers back to the genome (where k has been set to 36, 40, 50, 75 or 100 nucleotides to produce these tracks). For each window, a mappability score was computed (S = 1/(number of matches found in the genome): S=1 means one match in the genome, S=0.5 is two matches in the genome, and so on). The CRG Alignability tracks were generated independently of the ENCODE project, in the framework of the GEM (GEnome Multitool) project. Release Notes This is Release 1 (June 2012) of the ENCODE mappability track. It is a port of the old mappability track into the ENCODE format. There are no new datasets. Credits The CRG Alignability track was created by Thomas Derrien and Paolo Ribeca in Roderic Guigo's lab at the Centre for Genomic Regulation (CRG), Barcelona, Spain. TD was supported by funds from NHGRI for the ENCODE project, while PR was funded by a Consolider grant CDS2007-00050 from the Spanish Ministerio de Educaci&#243;n y Ciencia." 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. 
wgEncodeCrgMapabilityAlign100mer CRG Align 100 Mapability ENCODE June 2010 Freeze 2010-02-09 2010-11-09 wgEncodeEM002937 2937 Gingeras CRG-Guigo-m uniqueness no more than 2 mismatches wgEncodeCrgMapabilityAlign100mer Alignability Short Read Mappability Gingeras Guigo - CGR, Barcelona Displays how uniquely k-mer sequences align to a region of the genome. The GEM mapper (GEnome Multitool, CRG) maps sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts) allowing up to 2 mismatches. Mappability scores were computed as S = 1/(number of matches found in the genome). The CRG Alignability tracks were generated independently of the ENCODE project. Alignability of 100mers by GEM from ENCODE/CRG(Guigo) Mapping and Sequencing 
wgEncodeCrgMapabilityAlign75mer CRG Align 75 Mapability ENCODE June 2010 Freeze 2010-02-09 2010-11-09 wgEncodeEM002941 2941 Gingeras CRG-Guigo-m uniqueness no more than 2 mismatches wgEncodeCrgMapabilityAlign75mer Alignability Short Read Mappability Gingeras Guigo - CGR, Barcelona Displays how uniquely k-mer sequences align to a region of the genome. The GEM mapper (GEnome Multitool, CRG) maps sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts) allowing up to 2 mismatches. Mappability scores were computed as S = 1/(number of matches found in the genome). The CRG Alignability tracks were generated independently of the ENCODE project. Alignability of 75mers by GEM from ENCODE/CRG(Guigo) Mapping and Sequencing 
wgEncodeCrgMapabilityAlign50mer CRG Align 50 Mapability ENCODE June 2010 Freeze 2010-02-09 2010-11-09 wgEncodeEM002940 2940 Gingeras CRG-Guigo-m uniqueness no more than 2 mismatches wgEncodeCrgMapabilityAlign50mer Alignability Short Read Mappability Gingeras Guigo - CGR, Barcelona Displays how uniquely k-mer sequences align to a region of the genome. The GEM mapper (GEnome Multitool, CRG) maps sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts) allowing up to 2 mismatches. Mappability scores were computed as S = 1/(number of matches found in the genome). The CRG Alignability tracks were generated independently of the ENCODE project. Alignability of 50mers by GEM from ENCODE/CRG(Guigo) Mapping and Sequencing 
wgEncodeCrgMapabilityAlign40mer CRG Align 40 Mapability ENCODE June 2010 Freeze 2010-02-09 2010-11-09 wgEncodeEM002939 2939 Gingeras CRG-Guigo-m uniqueness no more than 2 mismatches wgEncodeCrgMapabilityAlign40mer Alignability Short Read Mappability Gingeras Guigo - CGR, Barcelona Displays how uniquely k-mer sequences align to a region of the genome. The GEM mapper (GEnome Multitool, CRG) maps sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts) allowing up to 2 mismatches. Mappability scores were computed as S = 1/(number of matches found in the genome). The CRG Alignability tracks were generated independently of the ENCODE project. Alignability of 40mers by GEM from ENCODE/CRG(Guigo) Mapping and Sequencing 
wgEncodeCrgMapabilityAlign36mer CRG Align 36 Mapability ENCODE June 2010 Freeze 2010-02-09 2010-11-09 wgEncodeEM002938 2938 Gingeras CRG-Guigo-m uniqueness no more than 2 mismatches wgEncodeCrgMapabilityAlign36mer Alignability Short Read Mappability Gingeras Guigo - CGR, Barcelona Displays how uniquely k-mer sequences align to a region of the genome. The GEM mapper (GEnome Multitool, CRG) maps sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts) allowing up to 2 mismatches. Mappability scores were computed as S = 1/(number of matches found in the genome). The CRG Alignability tracks were generated independently of the ENCODE project. Alignability of 36mers by GEM from ENCODE/CRG(Guigo) Mapping and Sequencing 
mgcFullMrna MGC Genes Mammalian Gene Collection Full ORF mRNAs Genes and Gene Predictions Description This track shows alignments of mouse mRNAs from the Mammalian Gene Collection (MGC) having full-length open reading frames (ORFs) to the genome. The goal of the Mammalian Gene Collection is to provide researchers with unrestricted access to sequence-validated full-length protein-coding cDNA clones for human, mouse, and rat genes. Display Conventions and Configuration The track follows the display conventions for gene prediction tracks. An optional codon coloring feature is available for quick validation and comparison of gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page. Methods GenBank mouse MGC mRNAs identified as having full-length ORFs were aligned against the genome using blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 1% of the best and at least 95% base identity with the genomic sequence were kept. Credits The mouse MGC full-length mRNA track was produced at UCSC from mRNA sequence data submitted to GenBank by the Mammalian Gene Collection project. References Mammalian Gene Collection project references. Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
jaxAllele MGI Allele Jackson Laboratory / Mouse Genome Informatics Allele Phenotype and Allele Description This track shows Mouse Genome Informatics (MGI) representative transcripts associated with MGI-curated alleles. Items are named by concatenating the representative transcript ID and allele symbol. All chemical- and radiation-induced alleles have been combined as type &quot;Induced.&quot; Floxed/Frt, reporter, knock-out and knock-in targeted alleles are combined as type &quot;Targeted.&quot; Random-expressed, random-gene disruption, and Cre/Flp transgenes are combined as type &quot;Transgenic&quot;. The other types included in this track are &quot;GeneTrapped&quot;, &quot;Spontaneous&quot; and &quot;Other&quot;. Methods The MGI database report MGI_PhenotypicAllele.rpt was parsed to provide a list of all curated alleles that have associated representative transcripts. Credits Thanks to MGI at The Jackson Laboratory, and Bob Sinclair in particular, for providing these data. 
jaxGeneTrap MGI Gene Trap Jackson Laboratory / Mouse Genome Informatics DNA and RNA Gene Traps Phenotype and Allele Description This track shows gene trap sequence tags from GenBank dbGSS that have an RNA-based sequence tag method (5'-RACE or 3'-RACE) or DNA-based sequence tag method. DNA-based gene trap sequence tags (purple) are derived from genomic DNA at the site of gene trap vector insertion. RNA-based gene trap sequence tags are derived from the exon adjacent to the insertion site. If the sequence tag method is 5'-RACE (blue), the insertion site is in the intron downstream from the most 3' exon represented in the sequence tag. If the sequence tag is 3'-RACE (green), the insertion site is in the intron upstream from the most 5' exon represented in the sequence tag. Gene trap mutagenesis requires that the vector inserts in the correct transcriptional orientation of the &quot;trapped&quot; gene. Sequence tags that overlap known genes in the opposite transcriptional orientation do not disrupt those genes from a gene trapping mechanism. Methods Sequence tags were collected from dbGSS and aligned to the reference genome by Mouse Genome Informatics (MGI) at The Jackson Laboratory. Credits Thanks to MGI at The Jackson Laboratory, and Bob Sinclair in particular, for providing these data. 
jaxPhenotype MGI Phenotype Jackson Laboratory / Mouse Genome Informatics Phenotype Phenotype and Allele Description This track shows Mouse Genome Informatics (MGI) representative transcripts associated with Mammalian Phenotype Ontology Top-Level terms. The terms have been abbreviated for display as follows: AbbreviationMPO Term Adipose adipose tissue phenotype Behavior behavior/neurological phenotype Cardiovascular cardiovascular system phenotype Cellular cellular phenotype Craniofacial craniofacial phenotype Digestive digestive/alimentary phenotype Embryogenesis embryogenesis phenotype Embryonic Lethal lethality-embryonic perinatal Gland endocrine/exocrine gland phenotype Growth Size growth/size phenotype Hearing/Ear hearing/vestibular/ear phenotype Hematopoietic hematopoietic system phenotype Homeostasis homeostasis/metabolism phenotype Immune immune system phenotype Integument integument phenotype Life Span life span-post-weaning/aging Limbs and Tail limbs/digits/tail phenotype Liver and Bile liver/biliary system phenotype Mortality mortality/aging Muscle muscle phenotype Nervous System nervous system phenotype Pigmentation pigmentation phenotype Postnatal Lethal lethality-postnatal Renal/Urinary renal/urinary system phenotype Reproductive reproductive system phenotype Respiratory respiratory system phenotype Skeleton skeleton phenotype Skin/Coat/Nails skin/coat/nails phenotype Taste/Smell taste/olfaction phenotype Touch touch/vibrissae phenotype Tumorigenesis tumorigenesis Vision/Eye vision/eye phenotype Methods The MGI database report MGI_PhenotypicAllele.rpt was parsed for markers and alleles that are associated with representative transcripts, and the Top-Level Mammalian Phenotype (MP) terms were captured. Note that these top-level terms can be associated with a marker multiple times (i.e. via multiple alleles). Credits Thanks to MGI at The Jackson Laboratory, and Bob Sinclair in particular, for providing these data. 
jaxQtl MGI QTL Quantitative Trait Loci From Jackson Laboratory / Mouse Genome Informatics Mapping and Sequencing Description This track shows approximate positions of quantitative trait loci based on reported peak LOD scores from Mouse Genome Informatics (MGI) at the Jackson Laboratory. Credits Thanks to MGI at the Jackson Laboratory, and Bob Sinclair in particular, for providing these data. 
jaxRepTranscript MGI RepTranscrpt Jackson Laboratory / Mouse Genome Informatics Representative Transcript Phenotype and Allele Description This track shows mappings of sequences chosen as &quot;best representative transcript&quot; for many highly curated Mouse Genome Informatics (MGI) genes. Representative transcript identifiers are a concatenation of the GenBank accession and the MGI gene symbol. Methods Representative transcript sequences were selected by MGI. The sequences were placed on the assembly using Blat and filtered to retain the single best hit. Credits Thanks to MGI at The Jackson Laboratory, and Bob Sinclair in particular, for providing these data. 
microsat Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats Variation and Repeats Description This track displays regions that are likely to be useful as microsatellite markers. These are sequences of at least 15 perfect di-nucleotide and tri-nucleotide repeats and tend to be highly polymorphic in the population. Methods The data shown in this track are a subset of the Simple Repeats track, selecting only those repeats of period 2 and 3, with 100% identity and no indels and with at least 15 copies of the repeat. The Simple Repeats track is created using the Tandem Repeats Finder. For more information about this program, see Benson (1999). Credits Tandem Repeats Finder was written by Gary Benson. References Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999 Jan 15;27(2):573-80. PMID: 9862982; PMC: PMC148217 
miRNA miRNA MicroRNAs from miRBase Genes and Gene Predictions Description The miRNA track shows microRNAs from miRBase. Display Conventions and Configuration The precursor forms of microRNAs (mirs) in the sense orientation are shown in black; those in the reverse orientation are colored grey. To display only those items that exceed a specific unnormalized score, enter a minimum score between 0 and 1000 in the text box at the top of the track description page. For this track, a score of 960 signifies that the miRNA is on the + strand and a score of 480 signifies that it is on the - strand. Methods Precursor miRNA genomic locations from miRBase were calculated using wublastn for sequence alignment with the requirement of 100% identity. The extents of the precursor sequences were not generally known, and were predicted based on base-paired hairpin structure. miRBase is described in Griffiths-Jones, S. et al. (2006). The miRNA Registry is described in Griffiths-Jones, S. (2004) and Weber, M.J. (2005) in the References section below. Credits Genome coordinates for this track were obtained from the miRBase sequences FTP site. References When making use of these data, please cite the folowing articles in addition to the primary sources of the miRNA sequences: Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008 Jan 1;36(Database issue):D154-8. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4. Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11. Weber MJ. New human and mouse microRNA genes found by homology search. Febs J. 2005 Jan;272(1):59-73. The following publication provides guidelines on miRNA annotation: Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M et al. A uniform system for microRNA annotation. RNA. 2003 Mar;9(3):277-9. 
est Mouse ESTs Mouse ESTs Including Unspliced mRNA and EST Description This track shows alignments between mouse expressed sequence tags (ESTs) in GenBank and the genome. ESTs are single-read sequences, typically about 500 bases in length, that usually represent fragments of transcribed genes. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality. The strand information (+/-) indicates the direction of the match between the EST and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the EST display. For example, to apply the filter to all ESTs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the &quot;tissue&quot; table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If &quot;and&quot; is selected, only ESTs that match all filter criteria will be highlighted. If &quot;or&quot; is selected, ESTs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display ESTs that match the filter criteria. If &quot;include&quot; is selected, the browser will display only those ESTs that match the filter criteria. This track may also be configured to display base labeling, a feature that allows the user to display all bases in the aligning sequence or only those that differ from the genomic sequence. For more information about this option, go to the Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods To make an EST, RNA is isolated from cells and reverse transcribed into cDNA. Typically, the cDNA is cloned into a plasmid vector and a read is taken from the 5' and/or 3' primer. For most &mdash; but not all &mdash; ESTs, the reverse transcription is primed by an oligo-dT, which hybridizes with the poly-A tail of mature mRNA. The reverse transcriptase may or may not make it to the 5' end of the mRNA, which may or may not be degraded. In general, the 3' ESTs mark the end of transcription reasonably well, but the 5' ESTs may end at any point within the transcript. Some of the newer cap-selected libraries cover transcription start reasonably well. Before the cap-selection techniques emerged, some projects used random rather than poly-A priming in an attempt to retrieve sequence distant from the 3' end. These projects were successful at this, but as a side effect also deposited sequences from unprocessed mRNA and perhaps even genomic sequences into the EST databases. Even outside of the random-primed projects, there is a degree of non-mRNA contamination. Because of this, a single unspliced EST should be viewed with considerable skepticism. To generate this track, mouse ESTs from GenBank were aligned against the genome using blat. Note that the maximum intron length allowed by blat is 750,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. When a single EST aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. Credits This track was produced at UCSC from EST sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
mrna Mouse mRNAs Mouse mRNAs from GenBank mRNA and EST Description The mRNA track shows alignments between mouse mRNAs in GenBank and the genome. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the &quot;tissue&quot; table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If &quot;and&quot; is selected, only mRNAs that match all filter criteria will be highlighted. If &quot;or&quot; is selected, mRNAs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display mRNAs that match the filter criteria. If &quot;include&quot; is selected, the browser will display only those mRNAs that match the filter criteria. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods GenBank mouse mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. Credits The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
nscanGene N-SCAN N-SCAN Gene Predictions Genes and Gene Predictions Description This track shows gene predictions using the N-SCAN gene structure prediction software provided by the Computational Genomics Lab at Washington University in St. Louis, MO, USA. Methods N-SCAN combines biological-signal modeling in the target genome sequence along with information from a multiple-genome alignment to generate de novo gene predictions. It extends the TWINSCAN target-informant genome pair to allow for an arbitrary number of informant sequences as well as richer models of sequence evolution. N-SCAN models the phylogenetic relationships between the aligned genome sequences, context-dependent substitution rates, insertions, and deletions. Mouse N-SCAN uses human (hg18) as the informant and iterative pseudogene masking. Credits Thanks to Michael Brent's Computational Genomics Group at Washington University St. Louis for providing this data. Special thanks for this implementation of N-SCAN to Aaron Tenney in the Brent lab, and Robert Zimmermann, currently at Max F. Perutz Laboratories in Vienna, Austria. References Gross SS, Brent MR. Using multiple alignments to improve gene prediction. J Comput Biol. 2006 Mar;13(2):379-93. PMID: 16597247 Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003 Oct 1;31(19):5654-66. PMID: 14500829; PMC: PMC206470 Korf I, Flicek P, Duan D, Brent MR. Integrating genomic homology into gene structure prediction. Bioinformatics. 2001;17 Suppl 1:S140-8. PMID: 11473003 van Baren MJ, Brent MR. Iterative gene prediction and pseudogene removal improves genome annotation. Genome Res. 2006 May;16(5):678-85. PMID: 16651666; PMC: PMC1457044 
wgEncodeNhgriBip NHGRI BiP Bip ENCODE July 2009 Freeze 2009-01-27 2009-10-27 Elnitski NHGRI-Elnitski wgEncodeNhgriBip Bidirectional Promoters Elnitski Elnitski - National Human Genome Research Institute ENCODE NHGRI Elnitski Bidirectional Promoters Expression and Regulation Description Bidirectional promoters are the regulatory regions that fall between pairs of genes, where the 5' ends of the genes within a pair are positioned in close proximity to one another. This spacing facilitates the initiation of transcription of both genes, creating two transcription forks that advance in opposite directions. The formal definition of a bidirectional promoter requires that the transcription initiation sites are separated by no more than 1,000 bp from one another. Using these criteria we have comprehensively annotated the human and mouse genomes for the presence of bidirectional promoters, using in silico approaches. The identification of these promoters is contingent upon the presence of adjacent, oppositely oriented pairs of genes, because few distinguishing features are available to uniquely identify bidirectional promoters de novo. Genomic annotations used for our identification phase include: A) UCSC known genes annotations (items with score=800). B) GenBank mRNA annotations (score=600). C) spliced ESTs (score=400). The annotations for protein coding genes (A) are strongly supported and therefore provide a high quality dataset for mapping bidirectional promoters. In contrast, bidirectional promoters supported by spliced ESTs (C) alone have varying levels of evidence, ranging from one characterized transcript to hundreds of them. For this reason, the mRNA annotation (B) from GenBank provides a stringent level of validation for the start sites of the EST transcripts. As a large class of regulatory sequences, bidirectional promoters exemplify a rich source of unexplored biological information in the human genome. When compared to the mouse genome, these promoters are identifiable as truly orthologous locations, being maintained in regions of conserved synteny (including both genes and the intervening promoter region) that have undergone no rearrangements since the last common ancestor of mammals, and in some cases fish. We use this approach to annotate orthologous bidirectional promoters in nonhuman species until genomic annotations become available. Methods Assigning Orthologous Regions A multi-stage approach to mapping orthology at bidirectional promoters was developed. Orthology assignments are strongest in coding regions. Therefore we began by mapping single human genes regulated by bidirectional promoters from the Known Genes annotations onto the mouse genome. Orthology assignments were determined using the "chains and nets" data from the UCSC Human Genome Browser mysql tables. Chains in the Genome Browser represent sequences of gapless aligned blocks. Nets provide a hierarchical ordering of those chains. Level 1 chains contain the longest, best-scoring sequence chains that span any selected region. Subsequent levels in the net represent the results of rearrangements, duplications, insertions and deletions that may have disrupted the presence of conserved synteny derived from an ancestral sequence. Confirming Orthologous Genes After determining the orthology assignments using the UCSC chains and nets data, we used the Known Gene annotations or spliced ESTs to search the identity of genes within the corresponding region. Known Genes represent protein-coding genes and therefore can be verified by chains and nets alignments, followed by confirmation of protein identity in both species. Spliced ESTs carry less descriptive information than protein coding genes and therefore were validated in the second species by their presence in an orthologous region, showing conserved synteny of the two genes within a pair, and meeting the criteria of less than 1,000 bp of intergenic distance between those transcripts. Our method for mapping bidirectional promoters in spliced EST datasets is described in more detail in a previous publication. If the program verified evidence for orthology and conserved-syntenic gene arrangement, then the orthologous bidirectional promoter was confirmed. After orthologous assignments were confirmed for pairs of human genes, the reciprocal assignments were analyzed from mouse to human. Currently orthologous bidirectional promoter regions (that have been identified using UCSC known genes) have been mapped in human, chimp, macaque, mouse, rat, dog and cow genomes). Credits These data were produced by Mary Q. Yang in the Elnitski lab at NHGRI, NIH. (contact: &#101;&#108;&#110;&#105;&#116;&#115;ki&#64;&#109;&#97;&#105;l.n&#105;&#104;.g&#111;&#118;) References Piontkivska H, Yang MQ, Larkin DM, Lewin HA, Reecy J, Elnitski L. Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts. BMC Genomics. 2009 Apr 24;10:189. PMID: 19393065; PMC: PMC2688522 Yang MQ, Elnitski LL. A computational study of bidirectional promoters in the human genome . Springer Lecture Series: Notes in Bioinformatics 2007. Yang MQ, Elnitski L. Orthology of Bidirectional Promoters Enables Use of a Multiple Class Predictor for Discriminating Functional Elements in the Human Genome. Proceedings of the 2007 International Conference on Bioinformatics &amp; Computational Biology. Proceedings of the 2007 International Conference on Bioinformatics &amp; Computational Biology . --> pp. 218-228. 2007. ISBN: 1-60132-042-6. Yang MQ, Koehly LM, Elnitski LL. Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes. PLoS Comput Biol. 2007 Apr 20;3(4):e72. PMID: 17447839; PMC: PMC1853124 Yang MQ, Taylor J, Elnitski L. Comparative analyses of bidirectional promoters in vertebrates. BMC Bioinformatics. 2008 May 28;9 Suppl 6:S9. PMID: 18541062; PMC: PMC2423431 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 tablemetadata as dateUnrestricted and on the download page. The full data release policy for ENCODE is available here. 
NIAGene NIA Gene Index NIA Mouse Gene Index Genes and Gene Predictions Description This track displays alignments of the National Institute on Aging (NIA) Mouse Gene Index (mm9) to the mouse genome. Methods The index was assembled from Blat alignments of the mouse genome (mm9/July 2007). See the NIA Mouse cDNA Project home page for more information. Credits This track was produced by Alexei A. Sharov, Dawood B. Dudekula and Minoru S. H. Ko at the NIA, National Institutes of Health. The research was supported by the NIA Intramural Research Program. References Sharov AA, Piao Y, Matoba R, Dudekula DB, Qian Y, VanBuren V, Falco G, Martin PR, Stagg CA, Bassey UC et al. Transcriptome analysis of mouse stem cells and early embryos. PLoS Biol. 2003 Dec;1(3):E74. PMID: 14691545; PMC: PMC300684 Sharov AA, Dudekula DB, Ko MS. Genome-wide assembly and analysis of alternative transcripts in mouse. Genome Res. 2005 May;15(5):748-54. PMID: 15867436; PMC: PMC1088304 
numtSeq NumtS Sequence Mouse NumtS mitochondrial sequence Variation and Repeats Description and display conventions NumtS (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear genomic sequences. The most credited hypothesis concerning their generation suggests that in presence of mutagenic agents, or under stress conditions, fragments of mtDNA escape from mitochondria, reach the nucleus and insert into chromosomes during break repair; although NumtS can also derive from duplication of genomic fragments. NumtS may be a cause of contamination during human mtDNA sequencing and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group chaired by M. Attimonelli (University of Bari, Italy) has produced the RMmsNumtS (Reference Mus musculus NumtS) compilation annotating 148 Mouse assembled NumtS. To allow the scientific community to access the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the group has designed the Mouse NumtS tracks described below. The NumtS tracks show nuclear and mitochondrial regions, based on the High Score Pairs (HSPs) obtained by aligning the mitochondrial reference genome (NC_005089) with the mm9 assembly of the mouse genome. "NumtS (Nuclear mitochondrial Sequences)" Track The "NumtS mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear genome. The shading of the items reflect the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts. "NumtS assembled" Track The "NumtS assembled" track shows items obtained by assembling HSPs annotated in the "NumtS" track fulfilling the following conditions: The orientation of their alignments must be concordant. The distance between them must be less than 2 kb, on the mitochondrial genome as well as on the nuclear genome. Exceptions for the second condition arise when a long repetitive element is present between two HSPs. "NumtS on mitochondrion" Track The "NumtS on mitochondrion" track shows the mapping of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the nuclear mapping is provided. "Mouse NumtS on mitochondrion SNP" Track The "Mouse NumtS SNP" shows the mapping of the HSPs on the mitochondrial genome, with the SNPs which fall within, derived from comparison with the mm9 assembly. No shading is here provided. For every item, a link pointing to the nuclear mapping is provided. Methods NumtS mappings were obtained by running Blast2seq (program: BlastN) between each chromosome of the Mouse Genome (mm9 assembly) and the mouse mitochondrial reference sequence (AC: NC_005089), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with spreadsheet interpolation and manual inspection. BED format is used for the first three annotation tracks, while for the last one the SAM/BAM format is preferred. Credits These data were provided by Francesco Maria Calabrese, Domenico Simone and Marcella Attimonelli from the Department of Biochemistry and Molecular Biology "Ernesto Quagliariello" (University of Bari, Italy). Manual inspection and format details are carried out by Francesco Maria Calabrese, Domenico Simone and Luana Raddi. References Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M. The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS. BMC Genomics. 2008 Jun 3;9:267. PMID: 18522722; PMC: PMC2447851 Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics. 2011 Oct 20;12:517. PMID: 22013967; PMC: PMC3228558 
bamMmsNumtSSorted NumtS SNPs Mouse NumtS on mitochondrion SNPs Variation and Repeats 
numtSMitochondrion NumtS on mitochon Mouse NumtS on mitochondrion Variation and Repeats Description and display conventions NumtS (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear genomic sequences. The most credited hypothesis concerning their generation suggests that in presence of mutagenic agents, or under stress conditions, fragments of mtDNA escape from mitochondria, reach the nucleus and insert into chromosomes during break repair; although NumtS can also derive from duplication of genomic fragments. NumtS may be a cause of contamination during human mtDNA sequencing and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group chaired by M. Attimonelli (University of Bari, Italy) has produced the RMmsNumtS (Reference Mus musculus NumtS) compilation annotating 148 Mouse assembled NumtS. To allow the scientific community to access the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the group has designed the Mouse NumtS tracks described below. The NumtS tracks show nuclear and mitochondrial regions, based on the High Score Pairs (HSPs) obtained by aligning the mitochondrial reference genome (NC_005089) with the mm9 assembly of the mouse genome. "NumtS (Nuclear mitochondrial Sequences)" Track The "NumtS mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear genome. The shading of the items reflect the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts. "NumtS assembled" Track The "NumtS assembled" track shows items obtained by assembling HSPs annotated in the "NumtS" track fulfilling the following conditions: The orientation of their alignments must be concordant. The distance between them must be less than 2 kb, on the mitochondrial genome as well as on the nuclear genome. Exceptions for the second condition arise when a long repetitive element is present between two HSPs. "NumtS on mitochondrion" Track The "NumtS on mitochondrion" track shows the mapping of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the nuclear mapping is provided. "Mouse NumtS on mitochondrion SNP" Track The "Mouse NumtS SNP" shows the mapping of the HSPs on the mitochondrial genome, with the SNPs which fall within, derived from comparison with the mm9 assembly. No shading is here provided. For every item, a link pointing to the nuclear mapping is provided. Methods NumtS mappings were obtained by running Blast2seq (program: BlastN) between each chromosome of the Mouse Genome (mm9 assembly) and the mouse mitochondrial reference sequence (AC: NC_005089), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with spreadsheet interpolation and manual inspection. BED format is used for the first three annotation tracks, while for the last one the SAM/BAM format is preferred. Credits These data were provided by Francesco Maria Calabrese, Domenico Simone and Marcella Attimonelli from the Department of Biochemistry and Molecular Biology "Ernesto Quagliariello" (University of Bari, Italy). Manual inspection and format details are carried out by Francesco Maria Calabrese, Domenico Simone and Luana Raddi. References Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M. The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS. BMC Genomics. 2008 Jun 3;9:267. PMID: 18522722; PMC: PMC2447851 Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics. 2011 Oct 20;12:517. PMID: 22013967; PMC: PMC3228558 
numtSAssembled NumtS assembled Mouse NumtS assembled Variation and Repeats Description and display conventions NumtS (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear genomic sequences. The most credited hypothesis concerning their generation suggests that in presence of mutagenic agents, or under stress conditions, fragments of mtDNA escape from mitochondria, reach the nucleus and insert into chromosomes during break repair; although NumtS can also derive from duplication of genomic fragments. NumtS may be a cause of contamination during human mtDNA sequencing and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group chaired by M. Attimonelli (University of Bari, Italy) has produced the RMmsNumtS (Reference Mus musculus NumtS) compilation annotating 148 Mouse assembled NumtS. To allow the scientific community to access the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the group has designed the Mouse NumtS tracks described below. The NumtS tracks show nuclear and mitochondrial regions, based on the High Score Pairs (HSPs) obtained by aligning the mitochondrial reference genome (NC_005089) with the mm9 assembly of the mouse genome. "NumtS (Nuclear mitochondrial Sequences)" Track The "NumtS mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear genome. The shading of the items reflect the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts. "NumtS assembled" Track The "NumtS assembled" track shows items obtained by assembling HSPs annotated in the "NumtS" track fulfilling the following conditions: The orientation of their alignments must be concordant. The distance between them must be less than 2 kb, on the mitochondrial genome as well as on the nuclear genome. Exceptions for the second condition arise when a long repetitive element is present between two HSPs. "NumtS on mitochondrion" Track The "NumtS on mitochondrion" track shows the mapping of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the nuclear mapping is provided. "Mouse NumtS on mitochondrion SNP" Track The "Mouse NumtS SNP" shows the mapping of the HSPs on the mitochondrial genome, with the SNPs which fall within, derived from comparison with the mm9 assembly. No shading is here provided. For every item, a link pointing to the nuclear mapping is provided. Methods NumtS mappings were obtained by running Blast2seq (program: BlastN) between each chromosome of the Mouse Genome (mm9 assembly) and the mouse mitochondrial reference sequence (AC: NC_005089), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with spreadsheet interpolation and manual inspection. BED format is used for the first three annotation tracks, while for the last one the SAM/BAM format is preferred. Credits These data were provided by Francesco Maria Calabrese, Domenico Simone and Marcella Attimonelli from the Department of Biochemistry and Molecular Biology "Ernesto Quagliariello" (University of Bari, Italy). Manual inspection and format details are carried out by Francesco Maria Calabrese, Domenico Simone and Luana Raddi. References Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M. The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS. BMC Genomics. 2008 Jun 3;9:267. PMID: 18522722; PMC: PMC2447851 Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics. 2011 Oct 20;12:517. PMID: 22013967; PMC: PMC3228558 
numtS NumtS Mouse NumtS Variation and Repeats Description and display conventions NumtS (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear genomic sequences. The most credited hypothesis concerning their generation suggests that in presence of mutagenic agents, or under stress conditions, fragments of mtDNA escape from mitochondria, reach the nucleus and insert into chromosomes during break repair; although NumtS can also derive from duplication of genomic fragments. NumtS may be a cause of contamination during human mtDNA sequencing and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group chaired by M. Attimonelli (University of Bari, Italy) has produced the RMmsNumtS (Reference Mus musculus NumtS) compilation annotating 148 Mouse assembled NumtS. To allow the scientific community to access the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the group has designed the Mouse NumtS tracks described below. The NumtS tracks show nuclear and mitochondrial regions, based on the High Score Pairs (HSPs) obtained by aligning the mitochondrial reference genome (NC_005089) with the mm9 assembly of the mouse genome. "NumtS (Nuclear mitochondrial Sequences)" Track The "NumtS mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear genome. The shading of the items reflect the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts. "NumtS assembled" Track The "NumtS assembled" track shows items obtained by assembling HSPs annotated in the "NumtS" track fulfilling the following conditions: The orientation of their alignments must be concordant. The distance between them must be less than 2 kb, on the mitochondrial genome as well as on the nuclear genome. Exceptions for the second condition arise when a long repetitive element is present between two HSPs. "NumtS on mitochondrion" Track The "NumtS on mitochondrion" track shows the mapping of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every item, a link pointing to the nuclear mapping is provided. "Mouse NumtS on mitochondrion SNP" Track The "Mouse NumtS SNP" shows the mapping of the HSPs on the mitochondrial genome, with the SNPs which fall within, derived from comparison with the mm9 assembly. No shading is here provided. For every item, a link pointing to the nuclear mapping is provided. Methods NumtS mappings were obtained by running Blast2seq (program: BlastN) between each chromosome of the Mouse Genome (mm9 assembly) and the mouse mitochondrial reference sequence (AC: NC_005089), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with spreadsheet interpolation and manual inspection. BED format is used for the first three annotation tracks, while for the last one the SAM/BAM format is preferred. Credits These data were provided by Francesco Maria Calabrese, Domenico Simone and Marcella Attimonelli from the Department of Biochemistry and Molecular Biology "Ernesto Quagliariello" (University of Bari, Italy). Manual inspection and format details are carried out by Francesco Maria Calabrese, Domenico Simone and Luana Raddi. References Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M. The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS. BMC Genomics. 2008 Jun 3;9:267. PMID: 18522722; PMC: PMC2447851 Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. BMC Genomics. 2011 Oct 20;12:517. PMID: 22013967; PMC: PMC3228558 
knownGeneOld4 Old UCSC Genes Previous Version of UCSC Genes Genes and Gene Predictions Description The Old UCSC Genes track shows genes from the previous version of the UCSC Genes build. This is similar to the current version is based on less Genbank, RefSeq, and UniProt data. Read the description of how the current version of the UCSC Genes track was built. 
oreganno ORegAnno Regulatory elements from ORegAnno Expression and Regulation Description This track displays literature-curated regulatory regions, transcription factor binding sites, and regulatory polymorphisms from ORegAnno (Open Regulatory Annotation). For more detailed information on a particular regulatory element, follow the link to ORegAnno from the details page. ORegAnno (Open Regulatory Annotation). --> Display Conventions and Configuration The display may be filtered to show only selected region types, such as: regulatory regions (shown in light blue) regulatory polymorphisms (shown in dark blue) transcription factor binding sites (shown in orange) regulatory haplotypes (shown in red) miRNA binding sites (shown in blue-green) To exclude a region type, uncheck the appropriate box in the list at the top of the Track Settings page. Methods An ORegAnno record describes an experimentally proven and published regulatory region (promoter, enhancer, etc.), transcription factor binding site, or regulatory polymorphism. Each annotation must have the following attributes: A stable ORegAnno identifier. A valid taxonomy ID from the NCBI taxonomy database. A valid PubMed reference. A target gene that is either user-defined, in Entrez Gene or in EnsEMBL. A sequence with at least 40 flanking bases (preferably more) to allow the site to be mapped to any release of an associated genome. At least one piece of specific experimental evidence, including the biological technique used to discover the regulatory sequence. (Currently only the evidence subtypes are supplied with the UCSC track.) A positive, neutral or negative outcome based on the experimental results from the primary reference. (Only records with a positive outcome are currently included in the UCSC track.) The following attributes are optionally included: A transcription factor that is either user-defined, in Entrez Gene or in EnsEMBL. A specific cell type for each piece of experimental evidence, using the eVOC cell type ontology. A specific dataset identifier (e.g. the REDfly dataset) that allows external curators to manage particular annotation sets using ORegAnno's curation tools. A &quot;search space&quot; sequence that specifies the region that was assayed, not just the regulatory sequence. A dbSNP identifier and type of variant (germline, somatic or artificial) for regulatory polymorphisms. Mapping to genome coordinates is performed periodically to current genome builds by BLAST sequence alignment. The information provided in this track represents an abbreviated summary of the details for each ORegAnno record. Please visit the official ORegAnno entry (by clicking on the ORegAnno link on the details page of a specific regulatory element) for complete details such as evidence descriptions, comments, validation score history, etc. Credits ORegAnno core team and principal contacts: Stephen Montgomery, Obi Griffith, and Steven Jones from Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada. The ORegAnno community (please see individual citations for various features): ORegAnno Citation. References Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL, Open Regulatory Annotation Consortium.. ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Res. 2016 Jan 4;44(D1):D126-32. PMID: 26578589; PMC: PMC4702855 Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13. PMID: 18006570; PMC: PMC2239002 Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics. 2006 Mar 1;22(5):637-40. PMID: 16397004 
orfeomeMrna ORFeome Clones ORFeome Collaboration Gene Clones Genes and Gene Predictions Description This track shows alignments of mouse clones from the ORFeome Collaboration. The goal of the project is to be an &quot;unrestricted source of fully sequence-validated full-ORF human cDNA clones in a format allowing easy transfer of the ORF sequences into virtually any type of expression vector. A major goal is to provide at least one fully-sequenced full-ORF clone for each human gene.&quot; This track is updated automatically as new clones become available. Display Conventions and Configuration The track follows the display conventions for gene prediction tracks. Methods ORFeome mouse clones were obtained from GenBank and aligned against the genome using the blat program. When a single clone aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. Credits and References Visit the ORFeome Collaboration members page for a list of credits and references. 
xenoMrna Other mRNAs Non-Mouse mRNAs from GenBank mRNA and EST Description This track displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank from organisms other than mouse. Display Conventions and Configuration This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality. The strand information (+/-) for this track is in two parts. The first + indicates the orientation of the query sequence whose translated protein produced the match (here always 5' to 3', hence +). The second + or - indicates the orientation of the matching translated genomic sequence. Because the two orientations of a DNA sequence give different predicted protein sequences, there are four combinations. ++ is not the same as --, nor is +- the same as -+. The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter: Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the &quot;tissue&quot; table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter. If filtering on more than one value, choose the desired combination logic. If &quot;and&quot; is selected, only mRNAs that match all filter criteria will be highlighted. If &quot;or&quot; is selected, mRNAs that match any one of the filter criteria will be highlighted. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If &quot;exclude&quot; is chosen, the browser will not display mRNAs that match the filter criteria. If &quot;include&quot; is selected, the browser will display only those mRNAs that match the filter criteria. This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page. Methods The mRNAs were aligned against the mouse genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% base identity with the genomic sequence were kept. Credits The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide. References Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518 
ucscGenePfam Pfam in UCSC Gene Pfam Domains in UCSC Genes Genes and Gene Predictions Description Most proteins are composed of one or more conserved functional regions called domains. This track shows the high-quality, manually-curated Pfam-A domains found in transcripts located in the UCSC Genes track by the software HMMER3. Display Conventions and Configuration This track follows the display conventions for gene tracks. Methods The sequences from the knownGenePep table (see UCSC Genes description page) are submitted to the set of Pfam-A HMMs which annotate regions within the predicted peptide that are recognizable as Pfam protein domains. These regions are then mapped to the transcripts themselves using the pslMap utility. A complete shell script log for every version of UCSC genes can be found in our GitHub repository under hg/makeDb/doc/ucscGenes, e.g. mm10.knownGenes17.csh is for the database mm10 and version 17 of UCSC known genes. Of the several options for filtering out false positives, the &quot;Trusted cutoff (TC)&quot; threshold method is used in this track to determine significance. For more information regarding thresholds and scores, see the HMMER documentation and results interpretation pages. Note: There is currently an undocumented but known HMMER problem which results in lessened sensitivity and possible missed searches for some zinc finger domains. Until a fix is released for HMMER /PFAM thresholds, please also consult the "UniProt Domains" subtrack of the UniProt track for more comprehensive zinc finger annotations. Credits pslMap was written by Mark Diekhans at UCSC. References Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K et al. The Pfam protein families database. Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. PMID: 19920124; PMC: PMC2808889 
polyASeqSites PolyA-Seq Poly(A)-sequencing from Merck Research Laboratories mRNA and EST Description This track displays the location of RNA polyadenylation (polyA) sites based on high-throughput RNA sequencing using the PolyA-seq protocol. PolyA-Seq data is strand-specific, therefore two tracks are provided for each tissue. PolyA site positions correspond to a single base, namely the ends of read alignments immediately upstream of the polyadenylation site. The data provided in this track consists of filtered polyA sites (see Methods). When multiple sites occurred within a 30-bp window on the same strand, the sum of the reads was attributed to the site with the most reads. Units are in reads per million (RPM) aligned. To obtain read counts, multiply RPM values by the total number of filtered reads for the corresponding experiment: Sample Filtered reads Brain 1187654 Kidney 3921370 Liver 4189409 Muscle 5517961 Testis 7466688 Display Conventions and Configuration These tracks may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page. For more information, see Configuring graph-based tracks. In the full and pack display modes, forward-strand tracks are shown in red and reverse-strand tracks are shown in black. In the squish and dense display modes, intensity is represented in grayscale (the darker the shading, the higher the intensity). To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. Methods A detailed explanation of the experimental methods is provided at NCBI's Gene Expression Omnibus under accession GSE30198. Briefly, PolyA+ RNA was reverse-transcribed using a T(10)VN primer and strand-specific universal adapters, amplified, and sequenced on an Illumina GAIIx sequencer. Reads were reverse-complemented, aligned to the corresponding reference genome and splice junctions, and retained only if they aligned uniquely. 3' ends of alignments were considered polyA sites. Sites were then filtered using downstream base frequency matrices for true- and false-positive sites determined from a modified experiment based on a T(10) primer (i.e., excluding the 3' VN). When multiple filtered sites occurred within a 30-nt window on the same strand, read counts were summed and attributed to the most abundant peak. For each tissue, read counts were then divided by the total number of reads, in millions, from all filtered sites. Credits These data were generated at Merck Research Laboratories and submitted by Adnan Derti and Tomas Babak. Data Release Policy No restrictions. 
polyASeqSitesSignalView Signal Poly(A)-sequencing from Merck Research Laboratories mRNA and EST 
polyASeqSitesTestisRev PolyA-Seq Testis Poly(A)-tail sequencing of Testis from Merck (Rev strand) mRNA and EST 
polyASeqSitesTestisFwd PolyA-Seq Testis Poly(A)-tail sequencing of Testis from Merck (Fwd strand) mRNA and EST 
polyASeqSitesMuscleRev PolyA-Seq Muscle Poly(A)-tail sequencing of Muscle from Merck (Rev strand) mRNA and EST 
polyASeqSitesMuscleFwd PolyA-Seq Muscle Poly(A)-tail sequencing of Muscle from Merck (Fwd strand) mRNA and EST 
polyASeqSitesLiverRev PolyA-Seq Liver Poly(A)-tail sequencing of Liver from Merck (Rev strand) mRNA and EST 
polyASeqSitesLiverFwd PolyA-Seq Liver Poly(A)-tail sequencing of Liver from Merck (Fwd strand) mRNA and EST 
polyASeqSitesKidneyRev PolyA-Seq Kidney Poly(A)-tail sequencing of Kidney from Merck (Rev strand) mRNA and EST 
polyASeqSitesKidneyFwd PolyA-Seq Kidney Poly(A)-tail sequencing of Kidney from Merck (Fwd strand) mRNA and EST 
polyASeqSitesBrainRev PolyA-Seq Brain Poly(A)-tail sequencing of Brain from Merck (Rev strand) mRNA and EST 
polyASeqSitesBrainFwd PolyA-Seq Brain Poly(A)-tail sequencing of Brain from Merck (Fwd strand) mRNA and EST 
wgEncodePsuDnase PSU DNaseI HS GSE40848 DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU Expression and Regulation Description Rationale for the Mouse ENCODE project Knowledge of the function of genomic DNA sequences comes from three basic approaches. Genetics uses changes in behavior or structure of a cell or organism in response to changes in DNA sequence to infer function of the altered sequence. Biochemical approaches monitor states of histone modification, binding of specific transcription factors, accessibility to DNases and other epigenetic features along genomic DNA. In general, these features are associated with gene activity, but the precise relationships remain to be established. The third approach is evolutionary, using comparisons among homologous DNA sequences to find segments that are evolving more slowly or more rapidly than expected given the local rate of neutral change. Such changes are inferred to be under negative or positive selection, respectively, and interpreted as DNA sequences needed for a preserved (negative selection) or adaptive (positive selection) function. The ENCODE project aims to discover all the DNA sequences associated with various epigenetic features, with the reasonable expectation that these will also be functional (best tested by genetic methods). However, it is not clear how to relate these results with those from evolutionary analyses. The mouse ENCODE project aims to make this connection explicitly and with a moderate breadth. Assays identical to those being used in the ENCODE project are performed in cell types in mouse that are similar or homologous to those studied in the human project. The comparison will be used to discover which epigenetic features are conserved between mouse and human, and examine the extent to which these overlap with the DNA sequences under negative selection. The contribution of functional DNA preserved in mammals versus function in only one species will be discovered. The results will have a significant impact on the understanding of the evolution of gene regulation. Maps of DNaseI Sensitivity DNaseI has long been used to map general chromatin accessibility, and DNaseI hypersensitivity is a universal feature of active cis-regulatory sequences. Maps of DNaseI sensitivity measured genome-wide are generated through DNaseI digestion, addition of linkers at the sites of cleavage, and library prep followed by massively parallel short read sequencing on the Illumina GAIIx and HiSeq platforms. The sequence tags are mapped back to the mouse genome, and a graph of the smoothed kernel density of DNaseI cleavage sites is displayed as the "Signal" track. This provides a quantitative estimate of the frequency of cleavage by DNaseI in the initial digest, which in turn is related to the accessibility of the DNA in the chromatin. Segments of greatest cleavage site density represent DNase hypersensitive sites (DHSs) and are identified as peaks by the F-seq program (Boyle et al. 2008). DHSs are candidates for any cis-regulatory module, including promoters, enhancers, insulators, and novel elements. 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. This track contains the following views: Peaks DNaseI hypersensitive sites (DHSs) identified as signal peaks. Peaks were called based on signals created using F-Seq, a software program developed at Duke (Boyle et al., 2008). Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. The solid vertical line in the peak represents the point with the highest signal. Signal Density graph (wiggle) of signal enrichment calculated using F-Seq for each replicate. F-Seq employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008). This method does not look at fixed-length windows, but rather weights contributions of nearby sequences in proportion to their distance from that base. Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks. Methods Cells were grown and harvested according to the approved ENCODE cell culture protocols for G1E and G1E-ER4. DNaseI hypersensitive sites were isolated using methods called DNase-seq or DNase-chip (Song and Crawford, 2010). Briefly, cells were lysed with NP40, and intact nuclei were digested with optimal levels of DNaseI enzyme. DNaseI-digested ends were captured from three different DNase concentrations, and material was sequenced using Illumina sequencing. The read length for sequences from DNase-seq is 20 bases long due to a MmeI cutting step of the approximately 50 kb DNA fragments extracted after DNaseI digestion. Sequences from each experiment were mapped to the mouse genome (mm9 assembly) using the program Bowtie (Langmead et al., 2009). Reads mapping to more than one location were not removed. For such reads, only the best mapping result was used ("--best" option). Sequences from multiple lanes were combined for a single replicate and converted to the sam/bam format using SAMtools. Using F-seq, the resulting digital signal was converted to a continuous wiggle track that employs a Parzen kernel density estimation to create base pair scores (Boyle et al., 2008). Discrete DNaseI HS sites (peaks) were identified from the DNase-seq F-seq density signal. Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Credits Cell growth and DNaseI digestion were done by Christine Dorman in the Hardison lab, and DNase-seq libraries were constructed in the laboratory of Greg Crawford (Duke). Sequencing was done by the laboratory of Greg Crawford (Duke). Data processing and analysis was done by Chris Morrissey (PSU) and Yoichiro Shibata (Duke) with advice from Terry Furey (University of North Carolina). Some analyses used tools provided in the Galaxy platform (Anton Nekrutenko, PSU, and James Taylor, Emory) enabled by the Penn State Cyberstar computer (supported by the National Science Foundation). Generation of these data was supported by National Institutes of Health grants R01DK065806 and RC2HG005573. Contact: Ross Hardison References 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. 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. 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 Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res. 2011 Oct;21(10):1659-71. 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. 
wgEncodePsuDnaseViewSignal Signal DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU Expression and Regulation 
wgEncodePsuDnaseG1eer4S129ME0Diffd24hSigRep2 G1E-ER4 E2 24 2 E0 G1E-ER4 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003047 3047 GSM1003238 Stam PSU-m 2 Illumina_HiSeq_2000 M 129 wgEncodePsuDnaseG1eer4S129ME0Diffd24hSigRep2 diffProtD_24hr Signal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) DNaseI HS Sequencing Stamatoyannopoulous Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 Estradiol 24hr DNaseI HS DNase-seq Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuDnaseG1eer4S129ME0Diffd24hSigRep1 G1E-ER4 E2 24 1 E0 G1E-ER4 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003047 3047 GSM1003238 Stam PSU-m 1 Illumina_GA2x M 129 wgEncodePsuDnaseG1eer4S129ME0Diffd24hSigRep1 diffProtD_24hr Signal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) DNaseI HS Sequencing Stamatoyannopoulous Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 Estradiol 24hr DNaseI HS Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuDnaseG1eS129ME0SigRep2 G1E 2 E0 G1E DnaseSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003046 3046 GSM1003239 Stam PSU-m 2 Illumina_HiSeq_2000 M 129 wgEncodePsuDnaseG1eS129ME0SigRep2 None Signal Embryonic day 0 (stem cell) Gata1- erythroid progenitor DNaseI HS Sequencing Stamatoyannopoulous Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Signal G1E DNaseI HS Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuDnaseG1eS129ME0SigRep1 G1E 1 E0 G1E DnaseSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003046 3046 GSM1003239 Stam PSU-m 1 Illumina_GA2x M 129 wgEncodePsuDnaseG1eS129ME0SigRep1 None Signal Embryonic day 0 (stem cell) Gata1- erythroid progenitor DNaseI HS Sequencing Stamatoyannopoulous Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Signal G1E DNaseI HS Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuDnaseViewPeaks Peaks DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU Expression and Regulation 
wgEncodePsuDnaseG1eer4S129ME0Diffd24hPkRep2 G1E-ER4 E2 24 2 E0 G1E-ER4 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003047 3047 GSM1003238 Stam PSU-m 2 Illumina_HiSeq_2000 M 129 wgEncodePsuDnaseG1eer4S129ME0Diffd24hPkRep2 diffProtD_24hr Peaks Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) DNaseI HS Sequencing Stamatoyannopoulous Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 Estradiol 24hr DNaseI HS DNase-seq Peaks Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuDnaseG1eer4S129ME0Diffd24hPkRep1 G1E-ER4 E2 24 1 E0 G1E-ER4 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003047 3047 GSM1003238 Stam PSU-m 1 Illumina_GA2x M 129 wgEncodePsuDnaseG1eer4S129ME0Diffd24hPkRep1 diffProtD_24hr Peaks Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) DNaseI HS Sequencing Stamatoyannopoulous Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 Estradiol 24hr DNaseI HS Peaks Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuDnaseG1eS129ME0PkRep2 G1E 2 E0 G1E DnaseSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003046 3046 GSM1003239 Stam PSU-m 2 Illumina_HiSeq_2000 M 129 wgEncodePsuDnaseG1eS129ME0PkRep2 None Peaks Embryonic day 0 (stem cell) Gata1- erythroid progenitor DNaseI HS Sequencing Stamatoyannopoulous Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E DNaseI HS Peaks Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuDnaseG1eS129ME0PkRep1 G1E 1 E0 G1E DnaseSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003046 3046 GSM1003239 Stam PSU-m 1 Illumina_GA2x M 129 wgEncodePsuDnaseG1eS129ME0PkRep1 None Peaks Embryonic day 0 (stem cell) Gata1- erythroid progenitor DNaseI HS Sequencing Stamatoyannopoulous Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E DNaseI HS Peaks Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistone PSU Histone GSE36028 Histone Modifications by ChIP-seq from ENCODE/PSU Expression and Regulation Description Rationale for the Mouse ENCODE project Knowledge of the function of genomic DNA sequences comes from three basic approaches. Genetics uses changes in behavior or structure of a cell or organism in response to changes in DNA sequence to infer function of the altered sequence. Biochemical approaches monitor states of histone modification, binding of specific transcription factors, accessibility to DNases and other epigenetic features along genomic DNA. In general, these are associated with gene activity, but the precise relationships remain to be established. The third approach is evolutionary, using comparisons among homologous DNA sequences to find segments that are evolving more slowly or more rapidly than expected given the local rate of neutral change. These are inferred to be under negative or positive selection, respectively, and interpreted as DNA sequences needed for a preserved (negative selection) or adaptive (positive selection) function. The ENCODE project aims to discover all the DNA sequences associated with various epigenetic features, with the reasonable expectation that these will also be functional &#40;best tested by genetic methods&#41;. However, it is not clear how to relate these results with those from evolutionary analyses. The mouse ENCODE project aims to make this connection explicitly and with a moderate breadth. Assays identical to those being used in the ENCODE project are performed in cell types in mouse that are similar or homologous to those studied in the human project. The comparison will be used to discover which epigenetic features are conserved between mouse and human, and examine the extent to which these overlap with the DNA sequences under negative selection. The contribution of functional DNA preserved in mammals versus function in only one species will be discovered. The results will have a significant impact on the understanding of the evolution of gene regulation. Maps of histone modifications Levels of five histone modifications were determined. Methylation of lysine 4 of histone H3 is associated with active chromatin, with monomethylation (H3K4me1) associated with enhancers and trimethylation (H3K4me3) associated with active promoters. Trimethylation of lysine 36 (H3K36me3) is associated with elongating RNA polymerase II. Two marks associated with repressed chromatin were also determined, trimethylation of lysine 27 of histone H3 (H3K27me3) which is deposited by Polycomb repressive complex 2, and trimethylation of lysine 9 of histone H3 (H3K9me3). Maps of genomic DNA in chromatin with these histone modifications are generated by ChIP-seq. This consists of two basic steps: chromatin immunoprecipitation (ChIP) is used to highly enrich genomic DNA for the segments bound by specific proteins (the antigens recognized by the antibodies) followed by massively parallel short read sequencing to tag the enriched DNA segments. Sequencing was done on the Illumina GAIIx and HiSeq. The sequence tags are mapped back to the mouse genome (&#40;Langmead et al., 2009&#41;), and a graph of the enrichment for histone modifications are displayed as the "Signal" track (essentially the counts of mapped reads per interval) and the deduced probable binding sites from the MACS program (&#40;Zhang et al., 2008&#41;) are shown in the "Peaks" track. Each experiment is associated with an input signal, which represents the control condition where immunoprecipitation with non-specific immunoglobulin was performed in the same cell type. 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. This track contains the following views: Peaks Regions of signal enrichment based on processed data (usually normalized data from pooled replicates). Intensity is represented in grayscale; the darker shading shows higher intensity (a solid vertical line in the peak region represents the point with the highest signal). ENCODE Peaks tables contain fields for statistical significance, including FDR (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. The chromatin immunoprecipitation followed published methods &#40;Welch et al., 2004&#41;. Information on antibodies used is available via the hyperlinks in the &#34;Select subtracks&#34; menu. Samples passing initial quality thresholds &#40;enrichment and depletion for positive and negative controls &#45; if available &#45; by quantitative PCR of ChIP material&#41; are processed for library construction for Illumina sequencing, using the ChIP-seq Sample Preparation Kit purchased from Illumina. Starting with a 10 ng sample of ChIP DNA, DNA fragments were repaired to generate blunt ends and a single A nucleotide was added to each end. Double-stranded Illumina adaptors were ligated to the fragments. Ligation products were amplified by 18 cycles of PCR, and the DNA between 250-350 bp was gel purified. Completed libraries were quantified with Quant-iT dsDNA HS Assay Kit. The DNA library was sequenced on the Illumina Genome Analyzer II sequencing system, and more recently on the HiSeq. Cluster generation, linearization, blocking and sequencing primer reagents were provided in the Illumina Cluster Amplification kits. All samples were determined as biological replicates except time course samples. The data displayed are from the pooled reads for all replicates, but individual replicates are available by download. The resulting 36-nucleotide sequence reads &#40;fastq files&#41; were moved to a data library in Galaxy, and the tools implemented in Galaxy were used for further processing via workflows &#40;Blankenberg et al., 2010&#41;. The reads were mapped to the mouse genome &#40;mm9 assembly&#41; using the program bowtie &#40;Langmead et al., 2009&#41;, and the files of mapped reads for the ChIP sample and from the &#34;input&#34; control &#40;no antibody&#41; were processed by MACs &#40;Zhang et al., 2008&#41; to call peaks for occupancy by transcription factors, using the parameters mfold=15, bandwidth=125. Since, the signal for some histone modifications is not expected to be tightly localized &#40;compared to a transcription factor&#41;, peak calling programs may not be appropriate. Thus in addition, we provide wiggle tracks with tag counts for every 10 bp segment. Per-replicate alignments and sequences are available for download at downloads page. Release Notes This is Release 2 (August 2012). It contains a total of 30 ChIP-seq experiments on Histone Modifications with the addition of 1 new experiment. Previous versions of files are available for download from the FTP site. Credits Cell growth, ChIP, and Illumina library construction were done primarily by Weisheng Wu, and sequencing on the Illumina platform was done largely by Cheryl Keller in the laboratory of Ross Hardison (PSU). Data processing and analysis were overseen by James Taylor (Emory University), using tools provided in the Galaxy platform (Anton Nekrutenko, PSU, and James Taylor, Emory) enabled by the Penn State Cyberstar computer (supported by the National Science Foundation). Generation of these data was supported by National Institutes of Health grants R01DK065806 and RC2HG005573. Contact: Ross Hardison References 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. Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A, Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. 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. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007 Mar;39(3):311-8. 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. M&#252;ller J, Hart CM, Francis NJ, Vargas ML, Sengupta A, Wild B, Miller EL, O'Connor MB, Kingston RE, Simon JA. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell. 2002 Oct 18;111(2):197-208. Rando OJ, Chang HY. Genome-wide views of chromatin structure. Annu Rev Biochem. 2009;78:245-71. Weiss MJ, Yu C, Orkin SH. Erythroid-cell-specific properties of transcription factor GATA-1 revealed by phenotypic rescue of a gene-targeted cell line. Mol Cell Biol. 1997 Mar;17(3):1642-51. Welch JJ, Watts JA, Vakoc CR, Yao Y, Wang H, Hardison RC, Blobel GA, Chodosh LA, Weiss MJ. Global regulation of erythroid gene expression by transcription factor GATA-1. Blood. 2004 Nov 15;104(10):3136-47. 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. Publications Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res. 2011 Oct;21(10):1659-71. 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. 
wgEncodePsuHistoneViewSignal Signal Histone Modifications by ChIP-seq from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneMegakaryoInputBE14halfCd1InputSig Megakary Input E14.5 Input Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002352 2352 GSM946539 Hardison PSU-m Illumina_HiSeq_2000 input B CD-1 wgEncodePsuHistoneMegakaryoInputBE14halfCd1InputSig Signal Embryonic day 14.5 Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Megakaryocyte Input Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneMegakaryoH3k36me3BE14halfCd1InputSig Megakary H3K36m3 E14.5 H3K36me3 Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-15 2012-08-15 wgEncodeEM002378 2378 GSM946540 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneMegakaryoH3k36me3BE14halfCd1InputSig Signal Embryonic day 14.5 Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Megakaryocyte H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneMegakaryoH3k27me3BE14halfCd1InputSig Megakary H3K27m3 E14.5 H3K27me3 Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-17 2012-08-17 wgEncodeEM002381 2381 GSM946523 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneMegakaryoH3k27me3BE14halfCd1InputSig Signal Embryonic day 14.5 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. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Megakaryocyte H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneMegakaryoH3k09me3BE14halfCd1InputSig Megakary H3K9m3 E14.5 H3K9me3 Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-15 2012-08-14 wgEncodeEM002379 2379 GSM946541 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneMegakaryoH3k09me3BE14halfCd1InputSig Signal Embryonic day 14.5 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. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Megakaryocyte H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneMegakaryoH3k04me3BE14halfCd1InputSig Megakary H3K4m3 E14.5 H3K4me3 Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-28 2012-07-28 wgEncodeEM002367 2367 GSM946527 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneMegakaryoH3k04me3BE14halfCd1InputSig Signal Embryonic day 14.5 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Megakaryocyte H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneMegakaryoH3k04me1BE14halfCd1InputSig Megakary H3K4m1 E14.5 H3K4me1 Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-30 2012-07-30 wgEncodeEM002369 2369 GSM946525 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneMegakaryoH3k04me1BE14halfCd1InputSig Signal Embryonic day 14.5 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Megakaryocyte H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eer4e2InputME0S129InputSig G1E-ER Input E0 Input G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-12-16 wgEncodeEM001921 1921 GSM946520 Hardison PSU-m Illumina_HiSeq_2000 input M 129 wgEncodePsuHistoneG1eer4e2InputME0S129InputSig diffProtD_24hr Signal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 Input Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eer4e2H3k36me3BE0S129InputSig G1E-ER H3K36m3 24 E0 H3K36me3 G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-30 2012-07-30 wgEncodeEM002368 2368 GSM946526 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eer4e2H3k36me3BE0S129InputSig diffProtD_24hr Signal Embryonic day 0 (stem cell) Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 H3K36me3 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eer4e2H3k27me3ME0S129InputSig G1E-ER H3K27m3 24 E0 H3K27me3 G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 wgEncodeEM001917 1917 GSM946537 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eer4e2H3k27me3ME0S129InputSig diffProtD_24hr Signal Embryonic day 0 (stem cell) 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. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 H3K27me3 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eer4e2H3k09me3ME0S129InputSig G1E-ER H3K9m3 24 E0 H3K9me3 G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-15 wgEncodeEM002377 2377 GSM946545 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eer4e2H3k09me3ME0S129InputSig diffProtD_24hr Signal Embryonic day 0 (stem cell) 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. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 H3K9me3 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eer4e2H3k04me3ME0S129InputSig G1E-ER H3K4m3 24 E0 H3K4me3 G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-26 2010-12-02 wgEncodeEM001920 1920 GSM946519 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eer4e2H3k04me3ME0S129InputSig diffProtD_24hr Signal Embryonic day 0 (stem cell) Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 H3K4me3 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eer4e2H3k04me1ME0S129InputSig G1E-ER H3K4m1 24 E0 H3K4me1 G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-11 wgEncodeEM001918 1918 GSM946534 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eer4e2H3k04me1ME0S129InputSig diffProtD_24hr Signal Embryonic day 0 (stem cell) Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 H3K4me1 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eInputME0S129InputSig G1E Input E0 Input G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-12-16 wgEncodeEM001916 1916 GSM946538 Hardison PSU-m Illumina_HiSeq_2000 input M 129 wgEncodePsuHistoneG1eInputME0S129InputSig Signal Embryonic day 0 (stem cell) Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Signal G1E Input Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eH3k36me3ME0S129InputSig G1E H3K36m3 E0 H3K36me3 G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-25 2012-07-24 wgEncodeEM002365 2365 GSM946529 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eH3k36me3ME0S129InputSig Signal Embryonic day 0 (stem cell) Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Signal G1E H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eH3k27me3ME0S129InputSig G1E H3K27m3 E0 H3K27me3 G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-09-30 wgEncodeEM002363 2363 GSM946531 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuHistoneG1eH3k27me3ME0S129InputSig Signal Embryonic day 0 (stem cell) 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. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Signal G1E H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eH3k09me3ME0S129InputSig G1E H3K9m3 E0 H3K9me3 G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-11 wgEncodeEM002374 2374 GSM946542 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eH3k09me3ME0S129InputSig Signal Embryonic day 0 (stem cell) 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. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Signal G1E H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eH3k04me3ME0S129InputSig G1E H3K4m3 E0 H3K4me3 G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-27 2010-12-02 wgEncodeEM001919 1919 GSM946533 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eH3k04me3ME0S129InputSig Signal Embryonic day 0 (stem cell) Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Signal G1E H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eH3k04me1ME0S129InputSig G1E H3K4m1 E0 H3K4me1 G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-31 2010-12-01 wgEncodeEM001915 1915 GSM946535 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eH3k04me1ME0S129InputSig Signal Embryonic day 0 (stem cell) Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Signal G1E H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneErythroblInputBE14halfCd1InputSig Erythrob Input E14.5 Input Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2011-12-14 wgEncodeEM002350 2350 GSM946544 Hardison PSU-m Illumina_HiSeq_2000 input B CD-1 wgEncodePsuHistoneErythroblInputBE14halfCd1InputSig Signal Embryonic day 14.5 Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Erythroblast Input Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneErythroblH3k36me3BE14halfCd1InputSig Erythrob H3K36m3 E14.5 H3K36me3 Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-15 2012-08-15 wgEncodeEM002375 2375 GSM946543 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneErythroblH3k36me3BE14halfCd1InputSig Signal Embryonic day 14.5 Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Erythroblast H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneErythroblH3k27me3BE14halfCd1InputSig Erythrob H3K27m3 E14.5 H3K27me3 Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-07 2012-08-07 wgEncodeEM002371 2371 GSM946547 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneErythroblH3k27me3BE14halfCd1InputSig Signal Embryonic day 14.5 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. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Erythroblast H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneErythroblH3k09me3BE14halfCd1InputSig Erythrob H3K9m3 E14.5 H3K9me3 Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-11 2012-08-11 wgEncodeEM002373 2373 GSM946549 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneErythroblH3k09me3BE14halfCd1InputSig Signal Embryonic day 14.5 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. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Erythroblast H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneErythroblH3k04me3BE14halfCd1InputSig Erythrob H3K4m3 E14.5 H3K4me3 Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-16 2012-08-15 wgEncodeEM002380 2380 GSM946524 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneErythroblH3k04me3BE14halfCd1InputSig Signal Embryonic day 14.5 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Erythroblast H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneErythroblH3k04me1BE14halfCd1InputSig Erythrob H3K4m1 E14.5 H3K4me1 Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-15 2012-08-15 wgEncodeEM002376 2376 GSM946536 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneErythroblH3k04me1BE14halfCd1InputSig Signal Embryonic day 14.5 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Erythroblast H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneCh12InputFImmortal2a4bInputSig CH12 Input immortalized Input CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2011-12-15 2012-09-15 wgEncodeEM001923 1923 GSM946521 Hardison PSU-m Illumina_HiSeq_2000 input F B10.H-2aH-4bp/Wts wgEncodePsuHistoneCh12InputFImmortal2a4bInputSig Signal Immortal cells B-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 Input Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneCh12H3k36me3FImmortal2a4bInputSig CH12 H3K36m3 immortalized H3K36me3 CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-25 2012-07-24 wgEncodeEM002364 2364 GSM946530 Hardison PSU-m Illumina_HiSeq_2000 exp F B10.H-2aH-4bp/Wts wgEncodePsuHistoneCh12H3k36me3FImmortal2a4bInputSig Signal Immortal cells 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-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneCh12H3k27me3FImmortal2a4bInputSig CH12 H3K27m3 immortalized H3K27me3 CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEM002362 2362 GSM946532 Hardison PSU-m Illumina_HiSeq_2000 exp F B10.H-2aH-4bp/Wts wgEncodePsuHistoneCh12H3k27me3FImmortal2a4bInputSig Signal Immortal cells 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-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneCh12H3k09me3FImmortal2a4bInputSig CH12 H3K9m3 immortalized H3K9me3 CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-11 2012-08-11 wgEncodeEM002372 2372 GSM946548 Hardison PSU-m Illumina_HiSeq_2000 exp F B10.H-2aH-4bp/Wts wgEncodePsuHistoneCh12H3k09me3FImmortal2a4bInputSig Signal Immortal cells 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-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneCh12H3k04me3FImmortal2a4bInputSig CH12 H3K4m3 immortalized H3K4me3 CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-28 2012-07-28 wgEncodeEM002366 2366 GSM946528 Hardison PSU-m Illumina_HiSeq_2000 exp F B10.H-2aH-4bp/Wts wgEncodePsuHistoneCh12H3k04me3FImmortal2a4bInputSig Signal Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneCh12H3k04me1FImmortal2a4bInputSig CH12 H3K4m1 immortalized H3K4me1 CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-31 2012-07-31 wgEncodeEM002370 2370 GSM946546 Hardison PSU-m Illumina_HiSeq_2000 exp F B10.H-2aH-4bp/Wts wgEncodePsuHistoneCh12H3k04me1FImmortal2a4bInputSig Signal Immortal cells Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. B-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneViewPeaks Peaks Histone Modifications by ChIP-seq from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneMegakaryoH3k36me3BE14halfCd1InputPk Megakary H3K36m3 E14.5 H3K36me3 Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-11-15 2012-08-15 wgEncodeEM002378 2378 GSM946540 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneMegakaryoH3k36me3BE14halfCd1InputPk Peaks Embryonic day 14.5 Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Megakaryocyte H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneMegakaryoH3k27me3BE14halfCd1InputPk Megakary H3K27m3 E14.5 H3K27me3 Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-11-17 2012-08-17 wgEncodeEM002381 2381 GSM946523 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneMegakaryoH3k27me3BE14halfCd1InputPk Peaks Embryonic day 14.5 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. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Megakaryocyte H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneMegakaryoH3k09me3BE14halfCd1InputPk Megakary H3K9m3 E14.5 H3K9me3 Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-11-15 2012-08-14 wgEncodeEM002379 2379 GSM946541 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneMegakaryoH3k09me3BE14halfCd1InputPk Peaks Embryonic day 14.5 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. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Megakaryocyte H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneMegakaryoH3k04me3BE14halfCd1InputPk Megakary H3K4m3 E14.5 H3K4me3 Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-10-28 2012-07-28 wgEncodeEM002367 2367 GSM946527 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneMegakaryoH3k04me3BE14halfCd1InputPk Peaks Embryonic day 14.5 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Megakaryocyte H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneMegakaryoH3k04me1BE14halfCd1InputPk Megakary H3K4m1 E14.5 H3K4me1 Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-10-30 2012-07-30 wgEncodeEM002369 2369 GSM946525 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneMegakaryoH3k04me1BE14halfCd1InputPk Peaks Embryonic day 14.5 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Megakaryocyte H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eer4e2H3k36me3BE0S129InputPk G1E-ER H3K36m3 24 E0 H3K36me3 G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-10-30 2012-07-30 wgEncodeEM002368 2368 GSM946526 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eer4e2H3k36me3BE0S129InputPk diffProtD_24hr Peaks Embryonic day 0 (stem cell) Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 H3K36me3 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eer4e2H3k27me3ME0S129InputPk G1E-ER H3K27m3 24 E0 H3K27me3 G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-09-23 wgEncodeEM001917 1917 GSM946537 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eer4e2H3k27me3ME0S129InputPk diffProtD_24hr Peaks Embryonic day 0 (stem cell) 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. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 H3K27me3 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eer4e2H3k09me3ME0S129InputPk G1E-ER H3K9m3 24 E0 H3K9me3 G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-11-15 wgEncodeEM002377 2377 GSM946545 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eer4e2H3k09me3ME0S129InputPk diffProtD_24hr Peaks Embryonic day 0 (stem cell) 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. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 H3K9me3 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eer4e2H3k04me3ME0S129InputPk G1E-ER H3K4m3 24 E0 H3K4me3 G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2010-12-02 wgEncodeEM001920 1920 GSM946519 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eer4e2H3k04me3ME0S129InputPk diffProtD_24hr Peaks Embryonic day 0 (stem cell) Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 H3K4me3 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eer4e2H3k04me1ME0S129InputPk G1E-ER H3K4m1 24 E0 H3K4me1 G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-11-11 wgEncodeEM001918 1918 GSM946534 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eer4e2H3k04me1ME0S129InputPk diffProtD_24hr Peaks Embryonic day 0 (stem cell) Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 H3K4me1 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eH3k36me3ME0S129InputPk G1E H3K36m3 E0 H3K36me3 G1E Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-10-25 2012-07-24 wgEncodeEM002365 2365 GSM946529 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eH3k36me3ME0S129InputPk Peaks Embryonic day 0 (stem cell) Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eH3k27me3ME0S129InputPk G1E H3K27m3 E0 H3K27me3 G1E Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-09-30 wgEncodeEM002363 2363 GSM946531 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuHistoneG1eH3k27me3ME0S129InputPk Peaks Embryonic day 0 (stem cell) 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. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eH3k09me3ME0S129InputPk G1E H3K9m3 E0 H3K9me3 G1E Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-11-11 wgEncodeEM002374 2374 GSM946542 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eH3k09me3ME0S129InputPk Peaks Embryonic day 0 (stem cell) 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. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eH3k04me3ME0S129InputPk G1E H3K4m3 E0 H3K4me3 G1E Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2010-12-02 wgEncodeEM001919 1919 GSM946533 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eH3k04me3ME0S129InputPk Peaks Embryonic day 0 (stem cell) Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneG1eH3k04me1ME0S129InputPk G1E H3K4m1 E0 H3K4me1 G1E Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-25 2010-12-01 wgEncodeEM001915 1915 GSM946535 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuHistoneG1eH3k04me1ME0S129InputPk Peaks Embryonic day 0 (stem cell) Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneErythroblH3k36me3BE14halfCd1InputPk Erythrob H3K36m3 E14.5 H3K36me3 Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-11-15 2012-08-15 wgEncodeEM002375 2375 GSM946543 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneErythroblH3k36me3BE14halfCd1InputPk Peaks Embryonic day 14.5 Specific for histone H3 tri methylated at lysine 36, weakly reacts with H3K36me2. Marks regions of RNAPII elongation, including coding and non-coding transcripts. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Erythroblast H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneErythroblH3k27me3BE14halfCd1InputPk Erythrob H3K27m3 E14.5 H3K27me3 Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-11-07 2012-08-07 wgEncodeEM002371 2371 GSM946547 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneErythroblH3k27me3BE14halfCd1InputPk Peaks Embryonic day 14.5 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. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Erythroblast H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneErythroblH3k09me3BE14halfCd1InputPk Erythrob H3K9m3 E14.5 H3K9me3 Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-11-11 2012-08-11 wgEncodeEM002373 2373 GSM946549 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneErythroblH3k09me3BE14halfCd1InputPk Peaks Embryonic day 14.5 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. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Erythroblast H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneErythroblH3k04me3BE14halfCd1InputPk Erythrob H3K4m3 E14.5 H3K4me3 Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-11-16 2012-08-15 wgEncodeEM002380 2380 GSM946524 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneErythroblH3k04me3BE14halfCd1InputPk Peaks Embryonic day 14.5 Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Erythroblast H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneErythroblH3k04me1BE14halfCd1InputPk Erythrob H3K4m1 E14.5 H3K4me1 Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-11-15 2012-08-15 wgEncodeEM002376 2376 GSM946536 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuHistoneErythroblH3k04me1BE14halfCd1InputPk Peaks Embryonic day 14.5 Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Erythroblast H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneCh12H3k36me3FImmortal2a4bInputPk CH12 H3K36m3 immortalized H3K36me3 CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-10-25 2012-07-24 wgEncodeEM002364 2364 GSM946530 Hardison PSU-m Illumina_HiSeq_2000 exp F B10.H-2aH-4bp/Wts wgEncodePsuHistoneCh12H3k36me3FImmortal2a4bInputPk Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneCh12H3k27me3FImmortal2a4bInputPk CH12 H3K27m3 immortalized H3K27me3 CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-09-23 2012-06-23 wgEncodeEM002362 2362 GSM946532 Hardison PSU-m Illumina_HiSeq_2000 exp F B10.H-2aH-4bp/Wts wgEncodePsuHistoneCh12H3k27me3FImmortal2a4bInputPk Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneCh12H3k09me3FImmortal2a4bInputPk CH12 H3K9m3 immortalized H3K9me3 CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-11-11 2012-08-11 wgEncodeEM002372 2372 GSM946548 Hardison PSU-m Illumina_HiSeq_2000 exp F B10.H-2aH-4bp/Wts wgEncodePsuHistoneCh12H3k09me3FImmortal2a4bInputPk Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneCh12H3k04me3FImmortal2a4bInputPk CH12 H3K4m3 immortalized H3K4me3 CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-10-28 2012-07-28 wgEncodeEM002366 2366 GSM946528 Hardison PSU-m Illumina_HiSeq_2000 exp F B10.H-2aH-4bp/Wts wgEncodePsuHistoneCh12H3k04me3FImmortal2a4bInputPk Peaks Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuHistoneCh12H3k04me1FImmortal2a4bInputPk CH12 H3K4m1 immortalized H3K4me1 CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2012-04-16 2011-10-31 2012-07-31 wgEncodeEM002370 2370 GSM946546 Hardison PSU-m Illumina_HiSeq_2000 exp F B10.H-2aH-4bp/Wts wgEncodePsuHistoneCh12H3k04me1FImmortal2a4bInputPk Peaks Immortal cells Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. B-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeq PSU RNA-seq GSE40522 RNA-seq from ENCODE/PSU Expression and Regulation Description Rationale for the Mouse ENCODE project Knowledge of the function of genomic DNA sequences comes from three basic approaches. Genetics uses changes in behavior or structure of a cell or organism in response to changes in DNA sequence to infer function of the altered sequence. Biochemical approaches monitor states of histone modification, binding of specific transcription factors, accessibility to DNases and other epigenetic features along genomic DNA. In general, these are associated with gene activity, but the precise relationships remain to be established. The third approach is evolutionary, using comparisons among homologous DNA sequences to find segments that are evolving more slowly or more rapidly than expected given the local rate of neutral change. These are inferred to be under negative or positive selection, respectively, and interpreted as DNA sequences needed for a preserved (negative selection) or adaptive (positive selection) function. The ENCODE project aims to discover all the DNA sequences associated with various epigenetic features, with the reasonable expectation that these will also be functional &#40;best tested by genetic methods&#41;. However, it is not clear how to relate these results with those from evolutionary analyses. The mouse ENCODE project aims to make this connection explicitly and with a moderate breadth. Assays identical to those being used in the ENCODE project are performed in cell types in mouse that are similar or homologous to those studied in the human project. Thus we will be able to discover which epigenetic features are conserved between mouse and human, and we can examine the extent to which these overlap with the DNA sequences under negative selection. The contribution of DNA with a function preserved in mammals versus that with a function in only one species will be discovered. Transcriptome Maps One of the epigenetic features most closely related to genomic activity is the production of stable RNA, including transcripts from both protein-coding genes and noncoding transcripts. These genomic compilations of transcripts, or transcriptomes, are primary determinants of the way cells function, respond and differentiate, both by the production of proteins translated from coding transcripts and the regulatory activity of untranslated non-coding transcripts. Non-coding RNA's regulate gene expression through diverse mechanisms ranging from reducing chromatin accessibility &#40;affecting large regions or whole chromosomes&#41; to precise fine-tuning of transcription from specific genes, e.g. via RNAi. Even though a large proportion of mammalian genomes is transcribed, many of the transcribed segments have yet to be assigned any function. The ENCODE project aims to create a comprehensive, quantitative annotation of the human transcriptome in several cell and tissue types as well as to understand regulation of transcriptomes by establishing the relationship between regulatory factors and their targets. Mapping the mouse transcriptome in similar tissues will allow us to discern conservation of transcriptome profiles between mouse and human and to discover species-specific transcription patterns, and to infer conserved versus species-specific regulatory mechanisms. The results will have a significant impact on our understanding of the evolution of gene regulation. 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. This track contains the following views: Raw SignalsThe Plus Raw Signal and Minus Raw Signal views show the density of mapped reads on the plus and minus strands (wiggle format), respectively. SignalDensity graph (wiggle) of signal enrichment based on processed data. AlignmentsMappings of short reads to 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. Total RNA was extracted from 5-10 million cells using TRIzol reagent. This was followed by mRNA selection, fragmentation and cDNA synthesis, which were performed as described previously &#40;Mortazavi et al., 2009&#41;. Double-stranded cDNA samples were processed for library construction for Illumina sequencing, using the Illumina ChIP-seq Sample Preparation Kit. Strand-specific libraries were generated in a similar manner, except for a couple of modifications described previously &#40;Parkhomchuk et al., 2009&#41;. Briefly, instead of dTTP, dUTP was used during second-strand cDNA synthesis to label the second-strand cDNA. During library preparation, the dUTP-labeled cDNA was treated with Uracil N Glycosylase, prior to the PCR amplification step. This was done to remove uracil from the second-strand, following which the DNA was subjected to high heat to facilitate abasic scission of the second strand. Cluster generation, linearization, blocking and sequencing primer reagents were provided in the Illumina Cluster Amplification kits. All samples are considered as biological replicates. Sequencing was done on the Illumina Genome Analyzer IIx and on the Illumina HiSeq 2000. FastQ files for the resulting sequence reads (single read and paired-end, directional and non-directional) were moved to a data library in Galaxy, and tools implemented in Galaxy were used for further processing via workflows (&#40;Giardine et al., 2005&#41;, &#40;Blankenberg et al., 2010 &#41;, &#40;Goecks et al., 2010&#41;). Data processing was also performed on the CyberSTAR high-performance computing system at Penn State. The reads were mapped to the mouse genome (mm9 assembly) using the program TopHat (&#40;Langmead et al., 2009&#41; and &#40;Trapnell et al., 2009&#41;). Signal tracks were created using BEDtools (Quinlan et al., 2010) and SAMtools (Li, Handasaker et al., 2009). Credits Cell growth and RNA isolation were done in the laboratories of Ross Hardison, Robert Paulson, David Bodine and Mitchell J. Weiss (PSU, NHGRI and Children's Hospital of Philadelphia). Isolation of mRNA, cDNA synthesis and Illumina library construction were done primarily by Tejaswini Mishra, and sequencing on the Illumina was done largely by Cheryl Keller, both in the laboratory of Ross Hardison. Mapping and transcript assembly were done by Belinda Giardine and Tejaswini Mishra on Galaxy and the CyberSTAR, Penn State high-performance computing system. Data processing and analysis were overseen by James Taylor (Emory University) and Ross Hardison (PSU). Generation of these data was supported by National Institutes of Health grants R01DK065806 and RC2HG005573. This work was supported in part through instrumentation funded by the National Science Foundation through grant OCI-0821527. Contact: Ross Hardison References Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005 Oct;15(10):1451-5. Goecks J, Nekrutenko A, Taylor J, Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11(8):R86. 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. 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. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. 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. 
wgEncodePsuRnaSeqViewSignal Signal RNA-seq from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dSigRep2 MEL DMSO 2% S 2 immortalized MEL RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEM003191 3191 GSM995526 Hardison PSU-m single cell 1x45 2 polyA Illumina_HiSeq_2000 M Unknown wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dSigRep2 DMSO_2.0pct Signal Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 45 nt reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL DMSO 2.0pct 1x45 RNA-seq Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dSigRep1 MEL DMSO 2% S 1 immortalized MEL RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEM003191 3191 GSM995526 Hardison PSU-m single cell 1x45 1 polyA Illumina_HiSeq_2000 M Unknown wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dSigRep1 DMSO_2.0pct Signal Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 45 nt reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL DMSO 2.0pct 1x45 RNA-seq Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMelMImmortalUknR1x45SigRep2 MEL S 2 immortalized MEL RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEM003190 3190 GSM995528 Hardison PSU-m single cell 1x45 2 polyA Illumina_HiSeq_2000 M Unknown wgEncodePsuRnaSeqMelMImmortalUknR1x45SigRep2 None Signal Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 45 nt reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Unknown strain origin Signal MEL 1x45 RNA-seq Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMelMImmortalUknR1x45SigRep1 MEL S 1 immortalized MEL RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEM003190 3190 GSM995528 Hardison PSU-m single cell 1x45 1 polyA Illumina_HiSeq_2000 M Unknown wgEncodePsuRnaSeqMelMImmortalUknR1x45SigRep1 None Signal Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 45 nt reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Unknown strain origin Signal MEL 1x45 RNA-seq Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hSigRep2 G1E-ER4 24hr S 2 E0 G1E-ER4 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEM003179 3179 GSM995529 Hardison PSU-m single cell 1x36 2 polyA Illumina_GA2x M 129 wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hSigRep2 diffProtD_24hr Signal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 36 nt reads Isolated Poly(A) RNA Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 Estradiol 24 hr 1x36 RNA-seq Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hSigRep1 G1E-ER4 24hr S 1 E0 G1E-ER4 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEM003179 3179 GSM995529 Hardison PSU-m single cell 1x36 1 polyA Illumina_GA2x M 129 wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hSigRep1 diffProtD_24hr Signal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 36 nt reads Isolated Poly(A) RNA Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 Estradiol 24 hr 1x36 RNA-seq Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eME0S129R1x55SigRep2 G1E S 2 E0 G1E RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEM003178 3178 GSM995530 Hardison PSU-m single cell 1x55 2 polyA Illumina_GA2x M 129 wgEncodePsuRnaSeqG1eME0S129R1x55SigRep2 None Signal Embryonic day 0 (stem cell) Gata1- erythroid progenitor Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 55 nt reads Isolated Poly(A) RNA Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Signal G1E single read (1x55) RNA-seq Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eME0S129R1x36SigRep1 G1E S 1 E0 G1E RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEM003178 3178 GSM995530 Hardison PSU-m single cell 1x36 1 polyA Illumina_GA2x M 129 wgEncodePsuRnaSeqG1eME0S129R1x36SigRep1 None Signal Embryonic day 0 (stem cell) Gata1- erythroid progenitor Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 36 nt reads Isolated Poly(A) RNA Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Signal G1E single read (1x36) RNA-seq Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41SigRep2 CH12 S 2 immortalized CH12 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEM003177 3177 GSM995540 Hardison PSU-m single cell 1x41 2 polyA Illumina_GA2x F B10.H-2aH-4bp/Wts wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41SigRep2 None Signal Immortal cells B-cell lymphoma (GM12878 analog) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 41 nt reads Isolated Poly(A) RNA Illumina Genome Analyzer IIx Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 1x41 RNA-seq Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41SigRep1 CH12 S 1 immortalized CH12 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEM003177 3177 GSM995540 Hardison PSU-m single cell 1x41 1 polyA Illumina_GA2x F B10.H-2aH-4bp/Wts wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41SigRep1 None Signal Immortal cells B-cell lymphoma (GM12878 analog) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 41 nt reads Isolated Poly(A) RNA Illumina Genome Analyzer IIx Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 1x41 RNA-seq Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqViewPlusRawSignal Plus Raw Signal RNA-seq from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dPlusRawRep2 MEP P 2 adult-5wks MEP RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003184 3184 GSM995525 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 F C57BL/6J wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dPlusRawRep2 None PlusRawSignal Adult 5 weeks mouse megakaryocyte erythroid progenitor cells with lineages CD16/32 and CD34- Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Female A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand MEP 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dPlusRawRep1 MEP P 1 adult-5wks MEP RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003184 3184 GSM995525 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 F C57BL/6J wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dPlusRawRep1 None PlusRawSignal Adult 5 weeks mouse megakaryocyte erythroid progenitor cells with lineages CD16/32 and CD34- Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Female A substrain of C57BL/6 Graphs the base-by-base density of tags on the plus strand MEP 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dPlusRawRep2 Megakaryocyte P 2 E14.5 Megakaryo RnaSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEM003193 3193 GSM995537 Hardison PSU-m paired-end Only ~2x3.5M reads mapped out of 2x101M total (low map %). But the coverage tracks resemble those of Megakaryo RNA Rep1, so this dataset was submitted cell 2x99D 2 polyA Illumina_HiSeq_2000 B CD-1 wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dPlusRawRep2 None PlusRawSignal Embryonic day 14.5 Megakaryocyte Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Graphs the base-by-base density of tags on the plus strand Megakaryocyte 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dPlusRawRep1 Megakaryocyte P 1 E14.5 Megakaryo RnaSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEM003193 3193 GSM995537 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 B CD-1 wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dPlusRawRep1 None PlusRawSignal Embryonic day 14.5 Megakaryocyte Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Graphs the base-by-base density of tags on the plus strand Megakaryocyte 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hPlusRawRep2 G1E-ER4 30hr P 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEM003192 3192 GSM995541 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hPlusRawRep2 diffProtD_30hr PlusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the plus strand G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hPlusRawRep1 G1E-ER4 30hr P 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEM003192 3192 GSM995541 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hPlusRawRep1 diffProtD_30hr PlusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the plus strand G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hPlusRawRep2 G1E-ER4 24hr P 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEM003189 3189 GSM995539 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hPlusRawRep2 diffProtD_24hr PlusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the plus strand G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hPlusRawRep1 G1E-ER4 24hr P 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEM003189 3189 GSM995539 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hPlusRawRep1 diffProtD_24hr PlusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the plus strand G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hPlusRawRep2 G1E-ER4 14hr P 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-24 wgEncodeEM003185 3185 GSM995527 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hPlusRawRep2 diffProtD_14hr PlusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 14 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the plus strand G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hPlusRawRep1 G1E-ER4 14hr P 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-24 wgEncodeEM003185 3185 GSM995527 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hPlusRawRep1 diffProtD_14hr PlusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 14 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the plus strand G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hPlusRawRep2 G1E-ER4 7hr P 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-24 wgEncodeEM003186 3186 GSM995531 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hPlusRawRep2 diffProtD_7hr PlusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the plus strand G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hPlusRawRep1 G1E-ER4 7hr P 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-24 wgEncodeEM003186 3186 GSM995531 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hPlusRawRep1 diffProtD_7hr PlusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the plus strand G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hPlusRawRep2 G1E-ER4 3hr P 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003188 3188 GSM995538 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hPlusRawRep2 diffProtD_3hr PlusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the plus strand G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hPlusRawRep1 G1E-ER4 3hr P 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003188 3188 GSM995538 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hPlusRawRep1 diffProtD_3hr PlusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the plus strand G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dPlusRawRep2 G1E-ER4 0hr P 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003187 3187 GSM995532 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dPlusRawRep2 None PlusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Graphs the base-by-base density of tags on the plus strand G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq  Plus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dPlusRawRep1 G1E-ER4 0hr P 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003187 3187 GSM995532 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dPlusRawRep1 None PlusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Graphs the base-by-base density of tags on the plus strand G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eME0S129R2x99dPlusRawRep2 G1E P 2 E0 G1E RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003183 3183 GSM995536 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eME0S129R2x99dPlusRawRep2 None PlusRawSignal Embryonic day 0 (stem cell) Gata1- erythroid progenitor Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Graphs the base-by-base density of tags on the plus strand G1E 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eME0S129R2x99dPlusRawRep1 G1E P 1 E0 G1E RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003183 3183 GSM995536 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eME0S129R2x99dPlusRawRep1 None PlusRawSignal Embryonic day 0 (stem cell) Gata1- erythroid progenitor Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Graphs the base-by-base density of tags on the plus strand G1E 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dPlusRawRep2 FV-progenitor P 2 adult-10-12wks FVprogenitor RnaSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003181 3181 GSM995534 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 B BALB/cJ wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dPlusRawRep2 None PlusRawSignal Adult between 8-10 weeks Friend virus infected murine CD34-,CD133-,Kit+,Sca1+ progenitor cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells A common inbred strain of laboratory mouse. Graphs the base-by-base density of tags on the plus strand FV-progenitor 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dPlusRawRep1 FV-progenitor P 1 adult-10-12wks FVprogenitor RnaSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003181 3181 GSM995534 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 B BALB/cJ wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dPlusRawRep1 None PlusRawSignal Adult between 8-10 weeks Friend virus infected murine CD34-,CD133-,Kit+,Sca1+ progenitor cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells A common inbred strain of laboratory mouse. Graphs the base-by-base density of tags on the plus strand FV-progenitor 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dPlusRawRep2 FVL-stem P 2 adult-10-12wks FVLstem RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003182 3182 GSM995535 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 B BALB/cJ wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dPlusRawRep2 None PlusRawSignal Adult between 8-10 weeks Friend virus infected murine CD34+,CD133+,Kit+,Sca1+ Leukemia stem cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells A common inbred strain of laboratory mouse. Graphs the base-by-base density of tags on the plus strand FVL-stem 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dPlusRawRep1 FVL-stem P 1 adult-10-12wks FVLstem RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003182 3182 GSM995535 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 B BALB/cJ wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dPlusRawRep1 None PlusRawSignal Adult between 8-10 weeks Friend virus infected murine CD34+,CD133+,Kit+,Sca1+ Leukemia stem cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells A common inbred strain of laboratory mouse. Graphs the base-by-base density of tags on the plus strand FVL-stem 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dPlusRawRep2 Erythroblast P 2 E14.5 Erythrobl RnaSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003180 3180 GSM995533 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 B CD-1 wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dPlusRawRep2 None PlusRawSignal Embryonic day 14.5 Erythroblast, ter119+ cells from liver Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Graphs the base-by-base density of tags on the plus strand Erythroblast 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dPlusRawRep1 Erythroblast P 1 E14.5 Erythrobl RnaSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003180 3180 GSM995533 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 B CD-1 wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dPlusRawRep1 None PlusRawSignal Embryonic day 14.5 Erythroblast, ter119+ cells from liver Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Graphs the base-by-base density of tags on the plus strand Erythroblast 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqViewMinusRawSignal Minus Raw Signal RNA-seq from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dMinusRawRep2 MEP M 2 adult-5wks MEP RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003184 3184 GSM995525 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 F C57BL/6J wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dMinusRawRep2 None MinusRawSignal Adult 5 weeks mouse megakaryocyte erythroid progenitor cells with lineages CD16/32 and CD34- Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Female A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand MEP 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dMinusRawRep1 MEP M 1 adult-5wks MEP RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003184 3184 GSM995525 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 F C57BL/6J wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dMinusRawRep1 None MinusRawSignal Adult 5 weeks mouse megakaryocyte erythroid progenitor cells with lineages CD16/32 and CD34- Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Female A substrain of C57BL/6 Graphs the base-by-base density of tags on the minus strand MEP 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dMinusRawRep2 Megakaryocyte M 2 E14.5 Megakaryo RnaSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEM003193 3193 GSM995537 Hardison PSU-m paired-end Only ~2x3.5M reads mapped out of 2x101M total (low map %). But the coverage tracks resemble those of Megakaryo RNA Rep1, so this dataset was submitted cell 2x99D 2 polyA Illumina_HiSeq_2000 B CD-1 wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dMinusRawRep2 None MinusRawSignal Embryonic day 14.5 Megakaryocyte Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Graphs the base-by-base density of tags on the minus strand Megakaryocyte  2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dMinusRawRep1 Megakaryocyte M 1 E14.5 Megakaryo RnaSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEM003193 3193 GSM995537 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 B CD-1 wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dMinusRawRep1 None MinusRawSignal Embryonic day 14.5 Megakaryocyte Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Graphs the base-by-base density of tags on the minus strand Megakaryocyte 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hMinusRawRep2 G1E-ER4 30hr M 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEM003192 3192 GSM995541 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hMinusRawRep2 diffProtD_30hr MinusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the minus strand G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hMinusRawRep1 G1E-ER4 30hr M 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEM003192 3192 GSM995541 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hMinusRawRep1 diffProtD_30hr MinusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the minus strand G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hMinusRawRep2 G1E-ER4 24hr M 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEM003189 3189 GSM995539 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hMinusRawRep2 diffProtD_24hr MinusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the minus strand G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hMinusRawRep1 G1E-ER4 24hr M 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEM003189 3189 GSM995539 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hMinusRawRep1 diffProtD_24hr MinusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the minus strand G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hMinusRawRep2 G1E-ER4 14hr M 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-24 wgEncodeEM003185 3185 GSM995527 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hMinusRawRep2 diffProtD_14hr MinusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 14 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the minus strand G1E-ER4 Estrdiol 14 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hMinusRawRep1 G1E-ER4 14hr M 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-24 wgEncodeEM003185 3185 GSM995527 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hMinusRawRep1 diffProtD_14hr MinusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 14 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the minus strand G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hMinusRawRep2 G1E-ER4 7hr M 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-24 wgEncodeEM003186 3186 GSM995531 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hMinusRawRep2 diffProtD_7hr MinusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the minus strand G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hMinusRawRep1 G1E-ER4 7hr M 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-24 wgEncodeEM003186 3186 GSM995531 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hMinusRawRep1 diffProtD_7hr MinusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the minus strand G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hMinusRawRep2 G1E-ER4 3hr M 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003188 3188 GSM995538 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hMinusRawRep2 diffProtD_3hr MinusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the minus strand G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hMinusRawRep1 G1E-ER4 3hr M 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003188 3188 GSM995538 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hMinusRawRep1 diffProtD_3hr MinusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Graphs the base-by-base density of tags on the minus strand G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dMinusRawRep2 G1E-ER4 0hr M 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003187 3187 GSM995532 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dMinusRawRep2 None MinusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Graphs the base-by-base density of tags on the minus strand G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dMinusRawRep1 G1E-ER4 0hr M 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003187 3187 GSM995532 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dMinusRawRep1 None MinusRawSignal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Graphs the base-by-base density of tags on the minus strand G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eME0S129R2x99dMinusRawRep2 G1E M 2 E0 G1E RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003183 3183 GSM995536 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eME0S129R2x99dMinusRawRep2 None MinusRawSignal Embryonic day 0 (stem cell) Gata1- erythroid progenitor Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Graphs the base-by-base density of tags on the minus strand G1E 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eME0S129R2x99dMinusRawRep1 G1E M 1 E0 G1E RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003183 3183 GSM995536 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eME0S129R2x99dMinusRawRep1 None MinusRawSignal Embryonic day 0 (stem cell) Gata1- erythroid progenitor Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Graphs the base-by-base density of tags on the minus strand G1E 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dMinusRawRep2 FV-progenitor M 2 adult-10-12wks FVprogenitor RnaSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003181 3181 GSM995534 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 B BALB/cJ wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dMinusRawRep2 None MinusRawSignal Adult between 8-10 weeks Friend virus infected murine CD34-,CD133-,Kit+,Sca1+ progenitor cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells A common inbred strain of laboratory mouse. Graphs the base-by-base density of tags on the minus strand FV-progenitor 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dMinusRawRep1 FV-progenitor M 1 adult-10-12wks FVprogenitor RnaSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003181 3181 GSM995534 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 B BALB/cJ wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dMinusRawRep1 None MinusRawSignal Adult between 8-10 weeks Friend virus infected murine CD34-,CD133-,Kit+,Sca1+ progenitor cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells A common inbred strain of laboratory mouse. Graphs the base-by-base density of tags on the minus strand FV-progenitor 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dMinusRawRep2 FVL-stem M 2 adult-10-12wks FVLstem RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003182 3182 GSM995535 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 B BALB/cJ wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dMinusRawRep2 None MinusRawSignal Adult between 8-10 weeks Friend virus infected murine CD34+,CD133+,Kit+,Sca1+ Leukemia stem cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells A common inbred strain of laboratory mouse. Graphs the base-by-base density of tags on the minus strand FVL-stem 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dMinusRawRep1 FVL-stem M 1 adult-10-12wks FVLstem RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003182 3182 GSM995535 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 B BALB/cJ wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dMinusRawRep1 None MinusRawSignal Adult between 8-10 weeks Friend virus infected murine CD34+,CD133+,Kit+,Sca1+ Leukemia stem cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells A common inbred strain of laboratory mouse. Graphs the base-by-base density of tags on the minus strand FVL-stem 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dMinusRawRep2 Erythroblast M 2 E14.5 Erythrobl RnaSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003180 3180 GSM995533 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 B CD-1 wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dMinusRawRep2 None MinusRawSignal Embryonic day 14.5 Erythroblast, ter119+ cells from liver Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Graphs the base-by-base density of tags on the minus strand Erythroblast 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dMinusRawRep1 Erythroblast M 1 E14.5 Erythrobl RnaSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003180 3180 GSM995533 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 B CD-1 wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dMinusRawRep1 None MinusRawSignal Embryonic day 14.5 Erythroblast, ter119+ cells from liver Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Graphs the base-by-base density of tags on the minus strand Erythroblast 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqViewAlignments Alignments RNA-seq from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dAlnRep2 MEP A 2 adult-5wks MEP RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003184 3184 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 F C57BL/6J wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dAlnRep2 None Alignments Adult 5 weeks mouse megakaryocyte erythroid progenitor cells with lineages CD16/32 and CD34- Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Female A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch MEP 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dAlnRep1 MEP A 1 adult-5wks MEP RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003184 3184 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 F C57BL/6J wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dAlnRep1 None Alignments Adult 5 weeks mouse megakaryocyte erythroid progenitor cells with lineages CD16/32 and CD34- Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Female A substrain of C57BL/6 Shows individual reads mapped to the genome and indicates where bases may mismatch MEP 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dAlnRep2 MEL DMSO 2% A 2 immortalized MEL RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEM003191 3191 Hardison PSU-m single cell 1x45 2 polyA Illumina_HiSeq_2000 M Unknown wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dAlnRep2 DMSO_2.0pct Alignments Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 45 nt reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Shows individual reads mapped to the genome and indicates where bases may mismatch MEL DMSO 2.0pct 1x45 RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dAlnRep1 MEL DMSO 2% A 1 immortalized MEL RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEM003191 3191 Hardison PSU-m single cell 1x45 1 polyA Illumina_HiSeq_2000 M Unknown wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dAlnRep1 DMSO_2.0pct Alignments Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 45 nt reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Shows individual reads mapped to the genome and indicates where bases may mismatch MEL DMSO 2.0pct 1x45 RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMelMImmortalUknR1x45AlnRep2 MEL A 2 immortalized MEL RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEM003190 3190 Hardison PSU-m single cell 1x45 2 polyA Illumina_HiSeq_2000 M Unknown wgEncodePsuRnaSeqMelMImmortalUknR1x45AlnRep2 None Alignments Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 45 nt reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Unknown strain origin Shows individual reads mapped to the genome and indicates where bases may mismatch MEL 1x45 RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMelMImmortalUknR1x45AlnRep1 MEL A 1 immortalized MEL RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-26 wgEncodeEM003190 3190 Hardison PSU-m single cell 1x45 1 polyA Illumina_HiSeq_2000 M Unknown wgEncodePsuRnaSeqMelMImmortalUknR1x45AlnRep1 None Alignments Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 45 nt reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Unknown strain origin Shows individual reads mapped to the genome and indicates where bases may mismatch MEL 1x45 RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dAlnRep2 Megakaryocyte A 2 E14.5 Megakaryo RnaSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEM003193 3193 Hardison PSU-m paired-end Only ~2x3.5M reads mapped out of 2x101M total (low map %). But the coverage tracks resemble those of Megakaryo RNA Rep1, so this dataset was submitted cell 2x99D 2 polyA Illumina_HiSeq_2000 B CD-1 wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dAlnRep2 None Alignments Embryonic day 14.5 Megakaryocyte Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Shows individual reads mapped to the genome and indicates where bases may mismatch Megakaryocyte 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dAlnRep1 Megakaryocyte A 1 E14.5 Megakaryo RnaSeq ENCODE Jul 2012 Freeze 2012-07-28 2013-04-28 wgEncodeEM003193 3193 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 B CD-1 wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dAlnRep1 None Alignments Embryonic day 14.5 Megakaryocyte Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Shows individual reads mapped to the genome and indicates where bases may mismatch Megakaryocyte 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hAlnRep2 G1E-ER4 30hr A 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEM003192 3192 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hAlnRep2 diffProtD_30hr Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hAlnRep1 G1E-ER4 30hr A 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-27 2013-04-27 wgEncodeEM003192 3192 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hAlnRep1 diffProtD_30hr Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hAlnRep2 G1E-ER4 24hr A 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEM003189 3189 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hAlnRep2 diffProtD_24hr Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hAlnRep1 G1E-ER4 24hr A 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-26 2013-04-25 wgEncodeEM003189 3189 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hAlnRep1 diffProtD_24hr Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hAlnRep2 G1E-ER4 14hr A 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-24 wgEncodeEM003185 3185 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hAlnRep2 diffProtD_14hr Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 14 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hAlnRep1 G1E-ER4 14hr A 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-24 wgEncodeEM003185 3185 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hAlnRep1 diffProtD_14hr Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 14 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hAlnRep2 G1E-ER4 7hr A 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-24 wgEncodeEM003186 3186 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hAlnRep2 diffProtD_7hr Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hAlnRep1 G1E-ER4 7hr A 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-24 wgEncodeEM003186 3186 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hAlnRep1 diffProtD_7hr Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hAlnRep2 G1E-ER4 3hr A 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003188 3188 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hAlnRep2 diffProtD_3hr Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hAlnRep1 G1E-ER4 3hr A 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003188 3188 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hAlnRep1 diffProtD_3hr Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dAlnRep2 G1E-ER4 0hr A 2 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003187 3187 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dAlnRep2 None Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R2x99dAlnRep1 G1E-ER4 0hr A 1 E0 G1E-ER4 RnaSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003187 3187 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eer4ME0S129R2x99dAlnRep1 None Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hAlnRep2 G1E-ER4 24hr A 2 E0 G1E-ER4 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEM003179 3179 Hardison PSU-m single cell 1x36 2 polyA Illumina_GA2x M 129 wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hAlnRep2 diffProtD_24hr Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 36 nt reads Isolated Poly(A) RNA Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 24 hr 1x36 RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hAlnRep1 G1E-ER4 24hr A 1 E0 G1E-ER4 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEM003179 3179 Hardison PSU-m single cell 1x36 1 polyA Illumina_GA2x M 129 wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hAlnRep1 diffProtD_24hr Alignments Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 36 nt reads Isolated Poly(A) RNA Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Shows individual reads mapped to the genome and indicates where bases may mismatch G1E-ER4 Estradiol 24 hr 1x36 RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eME0S129R2x99dAlnRep2 G1E A 2 E0 G1E RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003183 3183 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eME0S129R2x99dAlnRep2 None Alignments Embryonic day 0 (stem cell) Gata1- erythroid progenitor Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Shows individual reads mapped to the genome and indicates where bases may mismatch G1E 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eME0S129R2x99dAlnRep1 G1E A 1 E0 G1E RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003183 3183 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 M 129 wgEncodePsuRnaSeqG1eME0S129R2x99dAlnRep1 None Alignments Embryonic day 0 (stem cell) Gata1- erythroid progenitor Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Shows individual reads mapped to the genome and indicates where bases may mismatch G1E 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eME0S129R1x55AlnRep2 G1E A 2 E0 G1E RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEM003178 3178 Hardison PSU-m single cell 1x55 2 polyA Illumina_GA2x M 129 wgEncodePsuRnaSeqG1eME0S129R1x55AlnRep2 None Alignments Embryonic day 0 (stem cell) Gata1- erythroid progenitor Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 55 nt reads Isolated Poly(A) RNA Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Shows individual reads mapped to the genome and indicates where bases may mismatch G1E single read (1x55) RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqG1eME0S129R1x36AlnRep1 G1E A 1 E0 G1E RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEM003178 3178 Hardison PSU-m single cell 1x36 1 polyA Illumina_GA2x M 129 wgEncodePsuRnaSeqG1eME0S129R1x36AlnRep1 None Alignments Embryonic day 0 (stem cell) Gata1- erythroid progenitor Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 36 nt reads Isolated Poly(A) RNA Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Shows individual reads mapped to the genome and indicates where bases may mismatch G1E single read (1x36) RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dAlnRep2 FV-progenitor A 2 adult-10-12wks FVprogenitor RnaSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003181 3181 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 B BALB/cJ wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dAlnRep2 None Alignments Adult between 8-10 weeks Friend virus infected murine CD34-,CD133-,Kit+,Sca1+ progenitor cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells A common inbred strain of laboratory mouse. Shows individual reads mapped to the genome and indicates where bases may mismatch FV-progenitor 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dAlnRep1 FV-progenitor A 1 adult-10-12wks FVprogenitor RnaSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003181 3181 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 B BALB/cJ wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dAlnRep1 None Alignments Adult between 8-10 weeks Friend virus infected murine CD34-,CD133-,Kit+,Sca1+ progenitor cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells A common inbred strain of laboratory mouse. Shows individual reads mapped to the genome and indicates where bases may mismatch FV-progenitor 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dAlnRep2 FVL-stem A 2 adult-10-12wks FVLstem RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003182 3182 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 B BALB/cJ wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dAlnRep2 None Alignments Adult between 8-10 weeks Friend virus infected murine CD34+,CD133+,Kit+,Sca1+ Leukemia stem cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells A common inbred strain of laboratory mouse. Shows individual reads mapped to the genome and indicates where bases may mismatch FVL-stem 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dAlnRep1 FVL-stem A 1 adult-10-12wks FVLstem RnaSeq ENCODE Jul 2012 Freeze 2012-07-23 2013-04-22 wgEncodeEM003182 3182 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 B BALB/cJ wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dAlnRep1 None Alignments Adult between 8-10 weeks Friend virus infected murine CD34+,CD133+,Kit+,Sca1+ Leukemia stem cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells A common inbred strain of laboratory mouse. Shows individual reads mapped to the genome and indicates where bases may mismatch FVL-stem 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dAlnRep2 Erythroblast A 2 E14.5 Erythrobl RnaSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003180 3180 Hardison PSU-m paired-end cell 2x99D 2 polyA Illumina_HiSeq_2000 B CD-1 wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dAlnRep2 None Alignments Embryonic day 14.5 Erythroblast, ter119+ cells from liver Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Shows individual reads mapped to the genome and indicates where bases may mismatch Erythroblast 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dAlnRep1 Erythroblast A 1 E14.5 Erythrobl RnaSeq ENCODE Jul 2012 Freeze 2012-07-20 2013-04-20 wgEncodeEM003180 3180 Hardison PSU-m paired-end cell 2x99D 1 polyA Illumina_HiSeq_2000 B CD-1 wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dAlnRep1 None Alignments Embryonic day 14.5 Erythroblast, ter119+ cells from liver Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Paired 99 nt directed reads Isolated Poly(A) RNA Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Shows individual reads mapped to the genome and indicates where bases may mismatch Erythroblast 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41AlnRep2 CH12 A 2 immortalized CH12 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEM003177 3177 Hardison PSU-m single cell 1x41 2 polyA Illumina_GA2x F B10.H-2aH-4bp/Wts wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41AlnRep2 None Alignments Immortal cells B-cell lymphoma (GM12878 analog) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 41 nt reads Isolated Poly(A) RNA Illumina Genome Analyzer IIx Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Shows individual reads mapped to the genome and indicates where bases may mismatch CH12 1x41 RNA-seq Alignments Rep 2 from ENCODE/PSU Expression and Regulation 
wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41AlnRep1 CH12 A 1 immortalized CH12 RnaSeq ENCODE Mar 2012 Freeze 2012-03-28 2012-12-28 wgEncodeEM003177 3177 Hardison PSU-m single cell 1x41 1 polyA Illumina_GA2x F B10.H-2aH-4bp/Wts wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41AlnRep1 None Alignments Immortal cells B-cell lymphoma (GM12878 analog) Sequencing analysis of RNA expression Hardison Hardison - Penn State University Whole cell Single 41 nt reads Isolated Poly(A) RNA Illumina Genome Analyzer IIx Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Shows individual reads mapped to the genome and indicates where bases may mismatch CH12 1x41 RNA-seq Alignments Rep 1 from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbs PSU TFBS GSE36029 Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU Expression and Regulation Description Rationale for the Mouse ENCODE project Knowledge of the function of genomic DNA sequences comes from three basic approaches. Genetics uses changes in behavior or structure of a cell or organism in response to changes in DNA sequence to infer function of the altered sequence. Biochemical approaches monitor states of histone modification, binding of specific transcription factors, accessibility to DNases and other epigenetic features along genomic DNA. In general, these are associated with gene activity, but the precise relationships remain to be established. The third approach is evolutionary, using comparisons among homologous DNA sequences to find segments that are evolving more slowly or more rapidly than expected given the local rate of neutral change. These are inferred to be under negative or positive selection, respectively, and interpreted as DNA sequences needed for a preserved (negative selection) or adaptive (positive selection) function. The ENCODE project aims to discover all the DNA sequences associated with various epigenetic features, with the reasonable expectation that these will also be functional &#40;best tested by genetic methods&#41;. However, it is not clear how to relate these results with those from evolutionary analyses. The mouse ENCODE project aims to make this connection explicitly and with a moderate breadth. Assays identical to those being used in the ENCODE project are performed in cell types in mouse that are similar or homologous to those studied in the human project. The comparison will be used to discover which epigenetic features are conserved between mouse and human, and examine the extent to which these overlap with the DNA sequences under negative selection. The contribution of functional DNA preserved in mammals versus function with in only one species will be discovered. The results will have a significant impact on the understanding of the evolution of gene regulation. Maps of Occupancy by Transcription Factors Maps of occupancy of genomic DNA by transcription factors &#40;TFs&#41; are determined by ChIP-seq. This consists of two basic steps: chromatin immunoprecipitation &#40;ChIP&#41; is used to highly enrich genomic DNA for the segments bound by specific proteins &#40;the antigens recognized by the antibodies&#41; followed by massively parallel short read sequencing to tag the enriched DNA segments. Sequencing is done on the Illumina GAIIx and HiSeq. The sequence tags are mapped back to the mouse genome &#40;Langmead et al. 2009&#41;, and a graph of the enrichment for TF binding are displayed as the &#34;Signal&#34; track &#40;essentially the counts of mapped reads per interval&#41; and the deduced probable binding sites from the MACS program &#40;Zhang et al. 2008&#41; are shown in the &#34;Peaks&#34; track. Each experiment is associated with an input signal, which represents the control condition where immunoprecipitation with non-specific immunoglobulin was performed in the same cell type. 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. This track contains the following views: Peaks Regions of signal enrichment based on processed data (usually normalized data from pooled replicates). Intensity is represented in grayscale; the darker shading shows higher intensity (a solid vertical line in the peak region represents the point with the highest signal). ENCODE Peaks tables contain fields for statistical significance, including FDR (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. The chromatin immunoprecipitation followed published methods &#40;Welch et al. 2004&#41;. Information on antibodies used is available via the hyperlinks in the &#34;Select subtracks&#34; menu. Samples passing initial quality thresholds &#40;enrichment and depletion for positive and negative controls &#45; if available &#45; by quantitative PCR of ChIP material&#41; are processed for library construction for Illumina sequencing, using the ChIP-seq Sample Preparation Kit purchased from Illumina. Starting with a 10 ng sample of ChIP DNA, DNA fragments were repaired to generate blunt ends and a single A nucleotide was added to each end. Double-stranded Illumina adaptors were ligated to the fragments. Ligation products were amplified by 18 cycles of PCR, and the DNA between 250-350 bp was gel purified. Completed libraries were quantified with Quant-iT dsDNA HS Assay Kit. The DNA library was sequenced on the Illumina Genome Analyzer II sequencing system, and more recently on the HiSeq. Cluster generation, linearization, blocking and sequencing primer reagents were provided in the Illumina Cluster Amplification kits. All samples were determined as biological replicates except time course samples. The data displayed are from the pooled reads for all replicates, but individual replicates are available by download. The resulting 36-nucleotide sequence reads &#40;fastq files&#41; were moved to a data library in Galaxy, and the tools implemented in Galaxy were used for further processing via workflows &#40;Blankenberg et al. 2010&#41;. The reads were mapped to the mouse genome &#40;mm9 assembly&#41; using the program bowtie &#40;Langmead et al. 2009&#41;, and the files of mapped reads for the ChIP sample and from the &#34;input&#34; control &#40;no antibody&#41; were processed by MACs &#40;Zhang et al. 2008&#41; to call peaks for occupancy by transcription factors, using the parameters mfold=15, bandwidth=125. Per-replicate alignments and sequences are available for download at downloads page. Release Notes This is Release 2 (August 2012). It contains a total of 38 ChIP-seq experiments on Transcription Factor Binding Sites with the addition of 14 new experiments. One data set added an additional replicate: Megakaryocyte/GATA1_(SC-265) (UCSC Accession: wgEncodeEM002351). Files that have been reanalyzed have a version number appended to the name, e.g.V2. Previous versions of files are available for download from the FTP site. Credits Cell growth, ChIP, and Illumina library construction were done by researchers in the laboratories of Ross Hardison (PSU), Gerd Blobel and Mitch Weiss (Children's Hospital of Philadelphia); major contributors include Yong Cheng, Weisheng Wu, Deepti Jain, Cheryl Keller, Swathi Ashok Kumar, Tejaswini Mishra, Marta Byrska-Bishop, Stephan Kadauke, Maheshi Udugama, and Rena Zheng. Sequencing on the Illumina platform was done largely by Cheryl Keller in the laboratory of Ross Hardison (PSU). Data processing and analysis had major input from Chris Morrissey, Dan Blankenberg, and Belinda Giardine, as overseen by James Taylor (Emory University) and using tools provided in the Galaxy platform (Anton Nekrutenko, PSU, and James Taylor, Emory) enabled by the Penn State Cyberstar computer (supported by the National Science Foundation). Generation of these data was supported by National Institutes of Health grants R01DK065806 and RC2HG005573. Contact: Ross Hardison References Aplan PD, Nakahara K, Orkin SH, Kirsch IR. The SCL gene product: a positive regulator of erythroid differentiation. EMBO J. 1992 Nov;11(11):4073-81. Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A, Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. Green AR, DeLuca E, Begley CG. Antisense SCL suppresses self-renewal and enhances spontaneous erythroid differentiation of the human leukaemic cell line K562. EMBO J. 1991 Dec;10(13):4153-8. Huang S, Brandt SJ. mSin3A regulates murine erythroleukemia cell differentiation through association with the TAL1 (or SCL) transcription factor. Mol Cell Biol. 2000 Mar;20(6):2248-59. Huang S, Qiu Y, Shi Y, Xu Z, Brandt SJ. P/CAF-mediated acetylation regulates the function of the basic helix-loop-helix transcription factor TAL1/SCL. EMBO J. 2000 Dec 15;19(24):6792-803. 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. Shivdasani RA, Mayer EL, Orkin SH. Absence of blood formation in mice lacking the T-cell leukaemia oncoprotein tal-1/SCL. Nature. 1995 Feb 2;373(6513):432-4. Tripic T, Deng W, Cheng Y, Zhang Y, Vakoc CR, Gregory GD, Hardison RC, Blobel GA. SCL and associated proteins distinguish active from repressive GATA transcription factor complexes. Blood. 2009 Mar 5;113(10):2191-201. Wadman IA, Osada H, Gr&#252;tz GG, Agulnick AD, Westphal H, Forster A, Rabbitts TH. The LIM-only protein Lmo2 is a bridging molecule assembling an erythroid, DNA-binding complex which includes the TAL1, E47, GATA-1 and Ldb1/NLI proteins. EMBO J. 1997 Jun 2;16(11):3145-57. Weiss MJ, Yu C, Orkin SH. Erythroid-cell-specific properties of transcription factor GATA-1 revealed by phenotypic rescue of a gene-targeted cell line. Mol Cell Biol. 1997 Mar;17(3):1642-51. Welch JJ, Watts JA, Vakoc CR, Yao Y, Wang H, Hardison RC, Blobel GA, Chodosh LA, Weiss MJ. Global regulation of erythroid gene expression by transcription factor GATA-1. Blood. 2004 Nov 15;104(10):3136-47. Wold B, Myers RM. Sequence census methods for functional genomics. Nat Methods. 2008 Jan;5(1):19-21. 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. Publications Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res. 2011 Oct;21(10):1659-71. 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. 
wgEncodePsuTfbsViewSignal Signal Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMelInputUImmortalC57bl6InputSig MEL Input immortalized Input MEL Input ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2010-12-01 2011-08-30 wgEncodeEM001929 1929 GSM923574 Hardison PSU-m Illumina_HiSeq_2000 input M Unknown wgEncodePsuTfbsMelInputUImmortalC57bl6InputSig Signal Immortal cells Leukemia (K562 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Unknown strain origin Signal MEL Input TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMelTal1UImmortalC57bl6InputSig MEL TAL1 immortalized TAL1_(SC-12984) MEL Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-05 2012-08-05 wgEncodeEM002360 2360 GSM923578 Hardison PSU-m Illumina_HiSeq_2000 exp M Unknown wgEncodePsuTfbsMelTal1UImmortalC57bl6InputSig Signal Immortal cells TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. Leukemia (K562 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Unknown strain origin Signal MEL TAL1 TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputSig MEL Pol2 immortalized Pol2-4H8 MEL Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-10 2012-08-09 wgEncodeEM002361 2361 GSM923577 Hardison PSU-m Illumina_GA2x exp M Unknown wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputSig Signal Immortal cells This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. Leukemia (K562 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Unknown strain origin Signal MEL Pol2-4H8 TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputSig MEL CTCF immortalized CTCF MEL Input ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2010-12-01 2011-08-30 wgEncodeEM001928 1928 GSM923573 Hardison PSU-m Illumina_GA2x exp M Unknown wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputSig Signal Immortal cells CTCF zinc finger transcription factor. A sequence specific DNA binding 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 (K562 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Unknown strain origin Signal MEL CTCF TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMegakaryoInputBE14halfCd1InputSig Megakaryo Input E14.5 Input Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2011-08-18 2012-05-18 wgEncodeEM002352 2352 GSM923583 Hardison PSU-m Illumina_HiSeq_2000 input B CD-1 wgEncodePsuTfbsMegakaryoInputBE14halfCd1InputSig Signal Embryonic day 14.5 Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Megakaryocyte Input TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputSig Megakary TAL1 E14.5 TAL1_(SC-12984) Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM003194 3194 GSM995447 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputSig Signal Embryonic day 14.5 TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Megakaryocyte TAL1 TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputSigV2 Megakary GATA1 E14.5 GATA1_(SC-265) Megakaryo Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEM002351 2351 GSM923586 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputSigV2 Signal Embryonic day 14.5 GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Megakaryocyte GATA1 TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputSig Megakary FLI1 E14.5 FLI1_(sc-356) Megakaryo Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-18 wgEncodeEM003195 3195 GSM995446 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputSig Signal Embryonic day 14.5 Fli1 (Friend leukemia virus integration 1) is a member of a family of genes identified on the basis of their homology to the v-Ets oncogene isolated from the E26 erythoblastosis virus. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Megakaryocyte FLI1 TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4InputME0S129InputDiffd30hSigRep1 G1E-ER Input 30hr E0 Input G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003205 3205 GSM995438 Hardison PSU-m Timecourse 1 Illumina_HiSeq_2000 input M 129 wgEncodePsuTfbsG1eer4InputME0S129InputDiffd30hSigRep1 diffProtD_30hr Signal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 Input Estradiol 30 hr TC TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd30hSigRep1 G1E-ER GATA1 30hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003199 3199 GSM995448 Hardison PSU-m Timecourse 1 Illumina_HiSeq_2000 exp M 129 wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd30hSigRep1 diffProtD_30hr Signal Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 GATA1 Estradiol 30 hr TC TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4InputME0S129InputDiffd24hSigRep1 G1E-ER Input 24hr E0 Input G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003204 3204 GSM995439 Hardison PSU-m Timecourse 1 Illumina_HiSeq_2000 input M 129 wgEncodePsuTfbsG1eer4InputME0S129InputDiffd24hSigRep1 diffProtD_24hr Signal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 Input Estradiol 24 hr TC TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd24hSigRep1 G1E-ER GATA1 24hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003198 3198 GSM995449 Hardison PSU-m Timecourse 1 Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd24hSigRep1 diffProtD_24hr Signal Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 GATA1 Estradiol 24 hr TC TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4InputME0S129InputDiffd14hSigRep1 G1E-ER Input 14hr E0 Input G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003203 3203 GSM995440 Hardison PSU-m Timecourse 1 Illumina_HiSeq_2000 input M 129 wgEncodePsuTfbsG1eer4InputME0S129InputDiffd14hSigRep1 diffProtD_14hr Signal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 14 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 Input Estradiol 14 hr TC TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd14hSigRep1 G1E-ER GATA1 14hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003197 3197 GSM995444 Hardison PSU-m Timecourse 1 Illumina_HiSeq_2000 exp M 129 wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd14hSigRep1 diffProtD_14hr Signal Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 14 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 GATA1 Estradiol 14 hr TC TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4InputME0S129InputDiffd7hSigRep1 G1E-ER Input 7hr E0 Input G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003207 3207 GSM995436 Hardison PSU-m Timecourse 1 Illumina_HiSeq_2000 input M 129 wgEncodePsuTfbsG1eer4InputME0S129InputDiffd7hSigRep1 diffProtD_7hr Signal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 Input Estradiol 7 hr TC TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd7hSigRep1 G1E-ER GATA1 7hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003201 3201 GSM995442 Hardison PSU-m Timecourse 1 Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd7hSigRep1 diffProtD_7hr Signal Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 GATA1 Estradiol 7 hr TC TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4InputME0S129InputDiffd3hSigRep1 G1E-ER Input 3hr E0 Input G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003206 3206 GSM995437 Hardison PSU-m Timecourse 1 Illumina_HiSeq_2000 input M 129 wgEncodePsuTfbsG1eer4InputME0S129InputDiffd3hSigRep1 diffProtD_3hr Signal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 Input Estradiol 3 hr TC TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd3hSigRep1 G1E-ER GATA1 3hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003200 3200 GSM995443 Hardison PSU-m Timecourse 1 Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd3hSigRep1 diffProtD_3hr Signal Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 GATA1 Estradiol 3 hr TC TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4InputME0S129InputSigRep1 G1E-ER Input 0hr E0 Input G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003202 3202 GSM995441 Hardison PSU-m Timecourse 1 Illumina_HiSeq_2000 input M 129 wgEncodePsuTfbsG1eer4InputME0S129InputSigRep1 None Signal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Signal G1E-ER4 Input Estradiol 0 hr TC TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4Gata1aME0S129InputSigRep1 G1E-ER GATA1 0hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003196 3196 GSM995445 Hardison PSU-m Timecourse 1 Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4Gata1aME0S129InputSigRep1 None Signal Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Signal G1E-ER4 GATA1 Estradiol 0 hr TC TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4e2InputME0S129InputSig G1E-ER Input 24hr E0 Input G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-12-18 2010-11-28 wgEncodeEM001921 1921 GSM923567 Hardison PSU-m Illumina_HiSeq_2000 input M 129 wgEncodePsuTfbsG1eer4e2InputME0S129InputSig diffProtD_24hr Signal Embryonic day 0 (stem cell) Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 Input Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputSig G1E-ER TAL1 24hr E0 TAL1_(SC-12984) G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-15 wgEncodeEM002348 2348 GSM923576 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputSig diffProtD_24hr Signal Embryonic day 0 (stem cell) TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 TAL1 Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputSig G1E-ER Pol2 24hr E0 Pol2-4H8 G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEM002355 2355 GSM923590 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputSig diffProtD_24hr Signal Embryonic day 0 (stem cell) This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 Pol2-4H8 2hr Estradiol TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputSig G1E-ER GATA2 24hr E0 GATA2_(SC-9008) G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 wgEncodeEM002357 2357 GSM923588 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputSig diffProtD_24hr Signal Embryonic day 0 (stem cell) The GATA family of transcription factors share a conserved zinc finger DNA-binding domain and are capable of binding the WGATAR consensus sequence. GATA1 is erythroid-specific and is essential for normal erythropeisis. By comparison, GATA2 is expressed at high levels in hematopoeitic progenitors, including early erythroid cells, but is strong repressed during erythroblast differentiaion. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 GATA2 Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputSig G1E-ER GATA1 24hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-09 2010-11-26 wgEncodeEM001927 1927 GSM923572 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputSig diffProtD_24hr Signal Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 GATA1 Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4e2CtcfME0S129InputSig G1E-ER CTCF 24hr E0 CTCF G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-19 2010-11-26 2011-08-25 wgEncodeEM001926 1926 GSM923571 Hardison PSU-m http://main.g2.bx.psu.edu/u/kanwei/h/12nov2009ln3-ctcf-g1e-er4e2-groomed-canonical Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4e2CtcfME0S129InputSig diffProtD_24hr Signal Embryonic day 0 (stem cell) CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Signal G1E-ER4 CTCF Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eInputME0S129InputSig G1E Input E0 Input G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-12-16 2010-11-19 wgEncodeEM001916 1916 GSM923580 Hardison PSU-m Illumina_HiSeq_2000 input M 129 wgEncodePsuTfbsG1eInputME0S129InputSig Signal Embryonic day 0 (stem cell) Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Signal G1E Input TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eTal1ME0S129InputSig G1E TAL1 E0 TAL1_(SC-12984) G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-26 2011-02-11 wgEncodeEM001930 1930 GSM923579 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eTal1ME0S129InputSig Signal Embryonic day 0 (stem cell) TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Signal G1E TAL1 TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1ePol24h8ME0S129InputSig G1E Pol2 E0 Pol2-4H8 G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEM002354 2354 GSM923589 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuTfbsG1ePol24h8ME0S129InputSig Signal Embryonic day 0 (stem cell) This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Signal G1E Pol2-4H8 TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eGata2sc9008ME0S129InputSig G1E GATA2 E0 GATA2_(SC-9008) G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 wgEncodeEM002356 2356 GSM923587 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eGata2sc9008ME0S129InputSig Signal Embryonic day 0 (stem cell) The GATA family of transcription factors share a conserved zinc finger DNA-binding domain and are capable of binding the WGATAR consensus sequence. GATA1 is erythroid-specific and is essential for normal erythropeisis. By comparison, GATA2 is expressed at high levels in hematopoeitic progenitors, including early erythroid cells, but is strong repressed during erythroblast differentiaion. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Signal G1E GATA2 TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eGata1aME0S129InputSig G1E GATA1 E0 GATA1_(SC-265) G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEM002358 2358 GSM923581 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuTfbsG1eGata1aME0S129InputSig Signal Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Signal G1E GATA1 TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eCtcfME0S129InputSig G1E CTCF E0 CTCF G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-31 2010-11-19 2011-08-19 wgEncodeEM001925 1925 GSM923570 Hardison PSU-m http://main.g2.bx.psu.edu/u/kanwei/h/12nov2009ln4-ctcf-g1e-groomed-canonical Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eCtcfME0S129InputSig Signal Embryonic day 0 (stem cell) CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Signal G1E CTCF TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsErythroblInputBE14halfCd1InputSig Erythrobl Input E14.5 Input Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2011-12-15 2011-08-17 wgEncodeEM002350 2350 GSM923585 Hardison PSU-m Illumina_HiSeq_2000 input B CD-1 wgEncodePsuTfbsErythroblInputBE14halfCd1InputSig Signal Embryonic day 14.5 Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Erythroblast Input TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsErythroblTal1BE14halfCd1InputSig Erythrobl TAL1 E14.5 TAL1_(SC-12984) Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-01 wgEncodeEM002359 2359 GSM923582 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuTfbsErythroblTal1BE14halfCd1InputSig Signal Embryonic day 14.5 TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Erythroblast TAL1 TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputSig Erythrobl GATA1 E14.5 GATA1_(SC-265) Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-17 wgEncodeEM002349 2349 GSM923575 Hardison PSU-m Illumina_GA2x exp B CD-1 wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputSig Signal Embryonic day 14.5 GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal Erythroblast GATA1 TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsCh12InputFImmortal2a4bInputSig CH12 Input immortalized Input CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2011-12-15 2011-09-23 2012-06-23 wgEncodeEM001923 1923 GSM923569 Hardison PSU-m Illumina_HiSeq_2000 input F B10.H-2aH-4bp/Wts wgEncodePsuTfbsCh12InputFImmortal2a4bInputSig Signal Immortal cells B-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 Input TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputSig CH12 PAX5 immortalized PAX5_(N-15) CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEM002353 2353 GSM923584 Hardison PSU-m Illumina_HiSeq_2000 exp F B10.H-2aH-4bp/Wts wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputSig Signal Immortal cells The PAX5 gene is 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. The PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. The PAX5 gene encodes the B cell lineage specific activator protein (BSAP) that is expressed at early, but not late stages of B cell differentiation. B-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 PAX5 TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputSig CH12 CTCF immortalized CTCF CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2010-11-12 2011-08-12 wgEncodeEM001922 1922 GSM923568 Hardison PSU-m Illumina_GA2x exp F B10.H-2aH-4bp/Wts wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputSig Signal Immortal cells CTCF zinc finger transcription factor. A sequence specific DNA binding 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-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 CTCF TFBS ChIP-seq Signal from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsViewPeaks Peaks Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMelTal1UImmortalC57bl6InputPk MEL TAL1 immortalized TAL1_(SC-12984) MEL Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-05 2012-08-05 wgEncodeEM002360 2360 GSM923578 Hardison PSU-m Illumina_HiSeq_2000 exp M Unknown wgEncodePsuTfbsMelTal1UImmortalC57bl6InputPk Peaks Immortal cells TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. Leukemia (K562 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Unknown strain origin Regions of enriched signal in experiment MEL TAL1 TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputPk MEL Pol2 immortalized Pol2-4H8 MEL Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-10 2012-08-09 wgEncodeEM002361 2361 GSM923577 Hardison PSU-m Illumina_GA2x exp M Unknown wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputPk Peaks Immortal cells This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. Leukemia (K562 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Unknown strain origin Regions of enriched signal in experiment MEL Pol2 TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputPk MEL CTCF immortalized CTCF MEL Input ChipSeq ENCODE Mar 2012 Freeze 2011-09-08 2010-12-01 2011-08-30 wgEncodeEM001928 1928 GSM923573 Hardison PSU-m Illumina_GA2x exp M Unknown wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputPk Peaks Immortal cells CTCF zinc finger transcription factor. A sequence specific DNA binding 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 (K562 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Unknown strain origin Regions of enriched signal in experiment MEL CTCF TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputPk Megakary TAL1 E14.5 TAL1_(SC-12984) Megakaryo Input ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM003194 3194 GSM995447 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputPk Peaks Embryonic day 14.5 TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Megakaryocyte TAL1 TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputPkV2 Megakary GATA1 E14.5 GATA1_(SC-265) Megakaryo Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-17 2013-04-17 wgEncodeEM002351 2351 GSM923586 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputPkV2 Peaks Embryonic day 14.5 GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Megakaryocyte GATA1 TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputPk Megakary FLI1 E14.5 FLI1_(sc-356) Megakaryo Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-18 wgEncodeEM003195 3195 GSM995446 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputPk Peaks Embryonic day 14.5 Fli1 (Friend leukemia virus integration 1) is a member of a family of genes identified on the basis of their homology to the v-Ets oncogene isolated from the E26 erythoblastosis virus. Megakaryocyte Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Megakaryo FLI1 TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd30hPkRep1 G1E-ER GATA1 30hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003199 3199 GSM995448 Hardison PSU-m Timecourse 1 Illumina_HiSeq_2000 exp M 129 wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd30hPkRep1 diffProtD_30hr Peaks Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 GATA1 Estradiol 30 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd24hPkRep1 G1E-ER GATA1 24hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003198 3198 GSM995449 Hardison PSU-m Timecourse 1 Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd24hPkRep1 diffProtD_24hr Peaks Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 GATA1 Estradiol 24 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd14hPkRep1 G1E-ER GATA1 14hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003197 3197 GSM995444 Hardison PSU-m Timecourse 1 Illumina_HiSeq_2000 exp M 129 wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd14hPkRep1 diffProtD_14hr Peaks Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 14 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 GATA1 Estradiol 14 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd7hPkRep1 G1E-ER GATA1 7hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003201 3201 GSM995442 Hardison PSU-m Timecourse 1 Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd7hPkRep1 diffProtD_7hr Peaks Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 GATA1 Estradiol 7 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd3hPkRep1 G1E-ER GATA1 3hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003200 3200 GSM995443 Hardison PSU-m Timecourse 1 Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd3hPkRep1 diffProtD_3hr Peaks Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 GATA1 Estradiol 3 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4Gata1aME0S129InputPkRep1 G1E-ER GATA1 0hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003196 3196 GSM995445 Hardison PSU-m Timecourse 1 Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4Gata1aME0S129InputPkRep1 None Peaks Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E-ER4 GATA1 Estradiol 0 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputPk G1E-ER TAL1 24hr E0 TAL1_(SC-12984) G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-15 wgEncodeEM002348 2348 GSM923576 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputPk diffProtD_24hr Peaks Embryonic day 0 (stem cell) TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 TAL1 Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputPk G1E-ER Pol2 24hr E0 Pol2-4H8 G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEM002355 2355 GSM923590 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputPk diffProtD_24hr Peaks Embryonic day 0 (stem cell) This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 Pol2-4H8 Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputPk G1E-ER GATA2 24hr E0 GATA2_(SC-9008) G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 wgEncodeEM002357 2357 GSM923588 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputPk diffProtD_24hr Peaks Embryonic day 0 (stem cell) The GATA family of transcription factors share a conserved zinc finger DNA-binding domain and are capable of binding the WGATAR consensus sequence. GATA1 is erythroid-specific and is essential for normal erythropeisis. By comparison, GATA2 is expressed at high levels in hematopoeitic progenitors, including early erythroid cells, but is strong repressed during erythroblast differentiaion. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 GATA2 Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputPk G1E-ER GATA1 24hr E0 GATA1_(SC-265) G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-09 2010-11-26 wgEncodeEM001927 1927 GSM923572 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputPk diffProtD_24hr Peaks Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 GATA1 Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eer4e2CtcfME0S129InputPk G1E-ER CTCF 24hr E0 CTCF G1E-ER4 Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-19 2010-11-26 2011-08-25 wgEncodeEM001926 1926 GSM923571 Hardison PSU-m http://main.g2.bx.psu.edu/u/kanwei/h/12nov2009ln3-ctcf-g1e-er4e2-groomed-canonical Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eer4e2CtcfME0S129InputPk diffProtD_24hr Peaks Embryonic day 0 (stem cell) CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Gata1 restored erythroid cells, differentiation induced by estradiol (E2) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison) Regions of enriched signal in experiment G1E-ER4 CTCF Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eTal1ME0S129InputPk G1E TAL1 E0 TAL1_(SC-12984) G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-26 2011-02-11 wgEncodeEM001930 1930 GSM923579 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eTal1ME0S129InputPk Peaks Embryonic day 0 (stem cell) TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E TAL1 TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1ePol24h8ME0S129InputPk G1E Pol2 E0 Pol2-4H8 G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-09-26 2012-06-26 wgEncodeEM002354 2354 GSM923589 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuTfbsG1ePol24h8ME0S129InputPk Peaks Embryonic day 0 (stem cell) This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E Pol2-4H8 TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eGata2sc9008ME0S129InputPk G1E GATA2 E0 GATA2_(SC-9008) G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-21 wgEncodeEM002356 2356 GSM923587 Hardison PSU-m Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eGata2sc9008ME0S129InputPk Peaks Embryonic day 0 (stem cell) The GATA family of transcription factors share a conserved zinc finger DNA-binding domain and are capable of binding the WGATAR consensus sequence. GATA1 is erythroid-specific and is essential for normal erythropeisis. By comparison, GATA2 is expressed at high levels in hematopoeitic progenitors, including early erythroid cells, but is strong repressed during erythroblast differentiaion. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E GATA2 TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eGata1aME0S129InputPk G1E GATA1 E0 GATA1_(SC-265) G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-10-27 2012-07-27 wgEncodeEM002358 2358 GSM923581 Hardison PSU-m Illumina_HiSeq_2000 exp M 129 wgEncodePsuTfbsG1eGata1aME0S129InputPk Peaks Embryonic day 0 (stem cell) GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E GATA1 TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsG1eCtcfME0S129InputPk G1E CTCF E0 CTCF G1E Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-31 2010-11-19 2011-08-19 wgEncodeEM001925 1925 GSM923570 Hardison PSU-m http://main.g2.bx.psu.edu/u/kanwei/h/12nov2009ln4-ctcf-g1e-groomed-canonical Illumina_GA2x exp M 129 wgEncodePsuTfbsG1eCtcfME0S129InputPk Peaks Embryonic day 0 (stem cell) CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances. Gata1- erythroid progenitor Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Male Strain 129, has widely available embryonic stem cells Regions of enriched signal in experiment G1E CTCF TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsErythroblTal1BE14halfCd1InputPk Erythrobl TAL1 E14.5 TAL1_(SC-12984) Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2011-11-01 wgEncodeEM002359 2359 GSM923582 Hardison PSU-m Illumina_HiSeq_2000 exp B CD-1 wgEncodePsuTfbsErythroblTal1BE14halfCd1InputPk Peaks Embryonic day 14.5 TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Erythroblast TAL1 TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputPk Erythrobl GATA1 E14.5 GATA1_(SC-265) Erythrobl Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-17 wgEncodeEM002349 2349 GSM923575 Hardison PSU-m Illumina_GA2x exp B CD-1 wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputPk Peaks Embryonic day 14.5 GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes. Erythroblast, ter119+ cells from liver Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Both: a cell population with both male and female cells Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment Erythroblast GATA1 TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputPk CH12 PAX5 immortalized PAX5_(N-15) CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2011-09-23 2012-06-23 wgEncodeEM002353 2353 GSM923584 Hardison PSU-m Illumina_HiSeq_2000 exp F B10.H-2aH-4bp/Wts wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputPk Peaks Immortal cells The PAX5 gene is 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. The PAX proteins are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. The PAX5 gene encodes the B cell lineage specific activator protein (BSAP) that is expressed at early, but not late stages of B cell differentiation. B-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 PAX5 TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputPk CH12 CTCF immortalized CTCF CH12 Input ChipSeq ENCODE Mar 2012 Freeze 2011-08-30 2010-11-12 2011-08-12 wgEncodeEM001922 1922 GSM923568 Hardison PSU-m Illumina_GA2x exp F B10.H-2aH-4bp/Wts wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputPk Peaks Immortal cells CTCF zinc finger transcription factor. A sequence specific DNA binding 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-cell lymphoma (GM12878 analog) Control signal which may be subtracted from experimental raw signal before peaks are called. Chromatin IP Sequencing Hardison Hardison - Penn State University Illumina Genome Analyzer IIx Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 CTCF TFBS ChIP-seq Peaks from ENCODE/PSU Expression and Regulation 
rest REST Repressor Element 1-Silencing Transcription Factor (REST) binding sites Expression and Regulation Description This track contains genome-wide maps of Repressor Element 1-Silencing Transcription Factor (REST) binding sites in mouse stem cells, generated by the Stem Cell and Developmental Biology Group at the Genome Institute of Singapore. REST is a zinc finger transcriptional repressor that regulates a large cohort of neural genes throughout development. Aberrant REST activity has been implicated in various disease states, including cancer, epilepsy, Huntington's disease and cardiovascular disease. Display Conventions and Configuration The Embryonic Stem Cells only PET clusters (marked: ESC_only) are colored red. The Embryonic and Neural Stem Cells PET clusters (marked: ESC_NSC) are colored blue. Methods The ChIP-PET (chromatin immunoprecipitation coupled to paired-end di-tagging) method was used to identify genomic loci occupied by REST. 36 bp PETs generated from ChIP DNA fragments enriched for REST binding regions were sequenced using the high-throughput 454 sequencing technology. REST binding sites were defined as those having at least five overlapping PETs (PET5+). Mapping was carried out in two isogenic cell lines: the mouse embyronic stem cell E14, and the neural stem cell line NS5. The REST binding sites are divided into two categories: ESC and NSC shared sites, "ESC_NSC" (PET5+ in ESC, PET2+ in NSC) ESC-specific sites, "ESC_only" (PET5+ in ESC, PET&lt;2 in NSC) Negligible numbers of NS-only sites were identified. The coordinates displayed represent the PET minimal overlap region, defined as the region that is overlapped in common by all PETs constituting a cluster. Credits These data were generated by the Stanton Group at the Genome Institute of Singapore. References Johnson R, Teh CH, Kunarso G, Wong KY, Srinivasan G, Cooper ML, Volta M, Chan SS, Lipovich L, Pollard SM et al. REST regulates distinct transcriptional networks in embryonic and neural stem cells. PLoS Biol. 2008 Oct 28;6(10):e256. PMID: 18959480; PMC: PMC2573930 
genomicSuperDups Segmental Dups Duplications of >1000 Bases of Non-RepeatMasked Sequence Variation and Repeats Description This track shows regions detected as putative genomic duplications within the golden path. The following display conventions are used to distinguish levels of similarity: Light to dark gray: 90 - 98% similarity Light to dark yellow: 98 - 99% similarity Light to dark orange: greater than 99% similarity Red: duplications of greater than 98% similarity that lack sufficient Segmental Duplication Database evidence (most likely missed overlaps) For a region to be included in the track, at least 1 Kb of the total sequence (containing at least 500 bp of non-RepeatMasked sequence) had to align and a sequence identity of at least 90% was required. Methods Segmental duplications play an important role in both genomic disease and gene evolution. This track displays an analysis of the global organization of these long-range segments of identity in genomic sequence. Large recent duplications (&gt;= 1 kb and &gt;= 90% identity) were detected by identifying high-copy repeats, removing these repeats from the genomic sequence (&quot;fuguization&quot;) and searching all sequence for similarity. The repeats were then reinserted into the pairwise alignments, the ends of alignments trimmed, and global alignments were generated. For a full description of the &quot;fuguization&quot; detection method, see Bailey et al., 2001. This method has become known as WGAC (whole-genome assembly comparison); for example, see Bailey et al., 2002. Credits These data were provided by Ginger Cheng, Xinwei She, Archana Raja, Tin Louie and Evan Eichler at the University of Washington. References Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. Recent segmental duplications in the human genome. Science. 2002 Aug 9;297(5583):1003-7. PMID: 12169732 Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 2001 Jun;11(6):1005-17. PMID: 11381028; PMC: PMC311093 
sgpGene SGP Genes SGP Gene Predictions Using Mouse/Human Homology Genes and Gene Predictions Description This track shows gene predictions from the SGP2 homology-based gene prediction program developed by Roderic Guig&oacute;'s &quot;Computational Biology of RNA Processing&quot; group, which is part of the Centre de Regulaci&oacute; Gen&ograve;mica (CRG) in Barcelona, Catalunya, Spain. To predict genes in a genomic query, SGP2 combines geneid predictions with tblastx comparisons of the genome of the target species against genomic sequences of other species (reference genomes) deemed to be at an appropriate evolutionary distance from the target. Credits Thanks to the &quot;Computational Biology of RNA Processing&quot; group for providing these data. 
sibTxGraph SIB Alt-Splicing Alternative Splicing Graph from Swiss Institute of Bioinformatics mRNA and EST Description This track shows the graphs constructed by analyzing experimental RNA transcripts and serves as basis for the predicted alternative splicing transcripts shown in the SIB Genes track. The blocks represent exons; lines indicate introns. The graphical display is drawn such that no exons overlap, making alternative events easier to view when the track is in full display mode and the resolution is set to approximately gene-level. Further information on the graphs can be found on the Transcriptome Web interface. Methods The splicing graphs were generated using a multi-step pipeline: RefSeq and GenBank RNAs and ESTs are aligned to the genome with SIBsim4, keeping only the best alignments for each RNA. Alignments are broken up at non-intronic gaps, with small isolated fragments thrown out. A splicing graph is created for each set of overlapping alignments. This graph has an edge for each exon or intron, and a vertex for each splice site, start, and end. Each RNA that contributes to an edge is kept as evidence for that edge. Graphs consisting solely of unspliced ESTs are discarded. Credits The SIB Alternative Splicing Graphs track was produced on the Vital-IT high-performance computing platform using a computational pipeline developed by Christian Iseli with help from colleagues at the Ludwig Institute for Cancer Research and the Swiss Institute of Bioinformatics. It is based on data from NCBI RefSeq and GenBank/EMBL. Our thanks to the people running these databases and to the scientists worldwide who have made contributions to them. 
simpleRepeat Simple Repeats Simple Tandem Repeats by TRF Variation and Repeats Description This track displays simple tandem repeats (possibly imperfect repeats) located by Tandem Repeats Finder (TRF) which is specialized for this purpose. These repeats can occur within coding regions of genes and may be quite polymorphic. Repeat expansions are sometimes associated with specific diseases. Methods For more information about the TRF program, see Benson (1999). Credits TRF was written by Gary Benson. References Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999 Jan 15;27(2):573-80. PMID: 9862982; PMC: PMC148217 
wgEncodeSydhHist Stan/Yale Histone GSE32218 Histone Modifications by ChIP-seq from ENCODE/SYDH Expression and Regulation Description This track shows probable locations of the specified histone modifications in the given cell types as determined by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq). Each experiment is associated with an input signal which represents the control condition where immunoprecipitation with non-specific immunoglobulin was performed in the same cell type. For each experiment (cell type vs. antibody), this track shows a graph of enrichment for histone modification (Signal) along with sites that have the greatest evidence of histone modification, as identified by the PeakSeq algorithm (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. This track contains 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 FDR (qValue). SignalDensity graph (wiggle) of signal enrichment based on processed data. Methods Cells were grown according to the approved ENCODE cell culture protocols. For details on the chromatin immunoprecipitation protocol used, see Euskirchen et al. (2007), Rozowsky et al. (2009) and Auerbach 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 was 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;= 0.01 when comparing the number of peaks above said threshold to the number of peaks 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 was 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 had a p-value &lt;= 0.01 were considered to be significantly enriched compared to the input DNA control. Release Notes This is Release 2 (August 2012). It contains a total of 12 new experiments on histone modifications including 1 new cell line and 5 new antibodies. Errata At the request of the data provider, data files and table related to experiment wgEncodeEM003324 (H3K27ac in MEL cells) have been removed. An incorrect antibody was used in this experiment. Credits These data were generated and analyzed by the labs of Michael Snyder at Stanford University and Sherman Weissman at Yale University. &nbsp;&nbsp; Contact: Philip Cayting References Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefran&#231;ois P, Struhl K, Gerstein M, Snyder M. Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14926-31. 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. 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. 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. 
wgEncodeSydhHistViewSig Signal Histone Modifications by ChIP-seq from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelInputDm2p5dStdSig MEL Input DMSO immortalized Input MEL std ChipSeq ENCODE Jul 2012 Freeze 2012-08-15 2013-05-15 wgEncodeEM002791 2791 GSM1003758 Snyder Stanford-m PeakSeq1.0 input M Unknown wgEncodeSydhHistMelInputDm2p5dStdSig DMSO_2.0pct Signal Immortal cells Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL Input DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelInputIggyaleSig MEL Input Y immortalized Input MEL IgG-Yale ChipSeq ENCODE Mar 2012 Freeze 2010-04-26 2011-01-26 wgEncodeEM002003 2003 GSM798325 Snyder Yale-m PeakSeq1.0 input M Unknown wgEncodeSydhHistMelInputIggyaleSig None Signal Immortal cells Leukemia (K562 analog) Input signal from Mouse IgG ChIP-seq prepared at Yale Chromatin IP Sequencing Snyder Weissman - Yale University Male Unknown strain origin Signal MEL Input IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelInputDm2p5dIggyaleSig MEL Input DMSO Y immortalized Input MEL IgG-Yale ChipSeq ENCODE Mar 2012 Freeze 2011-06-16 2010-07-09 2011-04-09 wgEncodeEM001963 1963 GSM798323 Snyder Yale-m PeakSeq1.0 input M Unknown wgEncodeSydhHistMelInputDm2p5dIggyaleSig DMSO_2.0pct Signal Immortal cells Leukemia (K562 analog) Input signal from Mouse IgG ChIP-seq prepared at Yale Chromatin IP Sequencing Snyder Weissman - Yale University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL Input DMSO 2% IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelInputIggrabSig MEL Input rab immortalized Input MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-15 2013-05-15 wgEncodeEM001947 1947 GSM1003747 Snyder Stanford-m PeakSeq1.0 input M Unknown wgEncodeSydhHistMelInputIggrabSig None Signal Immortal cells Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL Input IgG-rab Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k36me3bDm2p5dStdSig MEL H3K36m3 DMSO immortalized H3K36me3B MEL std ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003332 3332 GSM1003749 Snyder Stanford-m exp M Unknown wgEncodeSydhHistMelH3k36me3bDm2p5dStdSig DMSO_2.0pct Signal Immortal cells Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL H3K36me3 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k27me3bDm2p5dStdSig MEL H3K27m3 DMSO immortalized H3K27me3B MEL std ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003331 3331 GSM1003745 Snyder Stanford-m exp M Unknown wgEncodeSydhHistMelH3k27me3bDm2p5dStdSig DMSO_2.0pct Signal Immortal cells Histone H3 (tri-methyl K27) marks repressed chromatin regions Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL H3K27me3 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k09me3IggrabSig MEL H3K9m3 rab immortalized H3K9me3 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM003327 3327 GSM1003755 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k09me3IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL H3K9me3 IgG-rab Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k09me3Dm2p5dStdSig MEL H3K9m3 DMSO immortalized H3K9me3 MEL std ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003333 3333 GSM1003748 Snyder Stanford-m exp M Unknown wgEncodeSydhHistMelH3k09me3Dm2p5dStdSig DMSO_2.0pct Signal Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL H3K9me3 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k4me3IggyaleSig MEL H3K4m3 Y immortalized H3K4me3 MEL IgG-Yale ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM002002 2002 GSM798324 Snyder Yale-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k4me3IggyaleSig None Signal Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Leukemia (K562 analog) Input signal from Mouse IgG ChIP-seq prepared at Yale Chromatin IP Sequencing Snyder Weissman - Yale University Male Unknown strain origin Signal MEL H3K4me3 IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k04me3IggrabSig MEL H3K4m3 rab immortalized H3K4me3 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM003325 3325 GSM1003753 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k04me3IggrabSig None Signal Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL H3K4me3 IgG-rab Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k04me3Dm2p5dIggyaleSig MEL H3K4m3 DMSO Y immortalized H3K4me3 MEL IgG-Yale ChipSeq ENCODE Mar 2012 Freeze 2011-04-20 2012-01-20 wgEncodeEM002005 2005 GSM798328 Snyder Yale-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k04me3Dm2p5dIggyaleSig DMSO_2.0pct Signal Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Leukemia (K562 analog) Input signal from Mouse IgG ChIP-seq prepared at Yale Chromatin IP Sequencing Snyder Weissman - Yale University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL H3K4me3 DMSO 2% IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k04me3Dm2p5dStdSig MEL H3K4m3 DMSO immortalized H3K4me3 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM003326 3326 GSM1003754 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k04me3Dm2p5dStdSig DMSO_2.0pct Signal Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL H3K4me3 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k04me1IggrabSig MEL H3K4m1 rab immortalized H3K4me1 MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-05-10 2013-02-10 wgEncodeEM003330 3330 GSM1003744 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k04me1IggrabSig None Signal Immortal cells Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL H3K4me1 IgG-rab Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k04me1Dm2p5dStdSig MEL H3K4m1 DMSO immortalized H3K4me1 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEM003329 3329 GSM1003757 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k04me1Dm2p5dStdSig DMSO_2.0pct Signal Immortal cells Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL H3K4me1 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistEse14InputStdSig ES-E14 Input E0 Input ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-08-15 2013-05-15 wgEncodeEM002788 2788 GSM1003746 Snyder Stanford-m PeakSeq1.0 input M 129/Ola wgEncodeSydhHistEse14InputStdSig None Signal Embryonic day 0 (stem cell) mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 Input Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistEse14H3k09me3StdSig ES-E14 H3K9m3 E0 H3K9me3 ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM003323 3323 GSM1003751 Snyder Stanford-m PeakSeq1.0 exp M 129/Ola wgEncodeSydhHistEse14H3k09me3StdSig None Signal Embryonic day 0 (stem cell) 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. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistEse14H3k04me3StdSig ES-E14 H3K4m3 E0 H3K4me3 ES-E14 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEM003328 3328 GSM1003756 Snyder Stanford-m PeakSeq1.0 exp M 129/Ola wgEncodeSydhHistEse14H3k04me3StdSig None Signal Embryonic day 0 (stem cell) Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistEse14H3k04me1StdSig ES-E14 H3K4m1 E0 H3K4me1 ES-E14 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM003322 3322 GSM1003750 Snyder Stanford-m PeakSeq1.0 exp M 129/Ola wgEncodeSydhHistEse14H3k04me1StdSig None Signal Embryonic day 0 (stem cell) Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistCh12InputIggyaleSig CH12 Input Y immortalized Input CH12 IgG-Yale ChipSeq ENCODE Mar 2012 Freeze 2010-05-12 2011-02-12 wgEncodeEM002001 2001 GSM798326 Snyder Yale-m PeakSeq1.0 input F B10.H-2aH-4bp/Wts wgEncodeSydhHistCh12InputIggyaleSig None Signal Immortal cells B-cell lymphoma (GM12878 analog) Input signal from Mouse IgG ChIP-seq prepared at Yale Chromatin IP Sequencing Snyder Weissman - Yale University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 Input IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistCh12H3k4me3IggyaleSig CH12 H3K4m3 Y immortalized H3K4me3 CH12 IgG-Yale ChipSeq ENCODE Mar 2012 Freeze 2010-05-12 2011-02-12 wgEncodeEM002004 2004 GSM798327 Snyder Yale-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhHistCh12H3k4me3IggyaleSig None Signal Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-cell lymphoma (GM12878 analog) Input signal from Mouse IgG ChIP-seq prepared at Yale Chromatin IP Sequencing Snyder Weissman - Yale University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 H3K4me3 IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistViewPeaks Peaks Histone Modifications by ChIP-seq from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k36me3bDm2p5dStdPk MEL H3K36m3 DMSO immortalized H3K36me3B MEL std ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003332 3332 GSM1003749 Snyder Stanford-m exp M Unknown wgEncodeSydhHistMelH3k36me3bDm2p5dStdPk DMSO_2.0pct Peaks Immortal cells Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Regions of enriched signal in experiment MEL H3K36me3 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k27me3bDm2p5dStdPk MEL H3K27m3 DMSO immortalized H3K27me3B MEL std ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003331 3331 GSM1003745 Snyder Stanford-m exp M Unknown wgEncodeSydhHistMelH3k27me3bDm2p5dStdPk DMSO_2.0pct Peaks Immortal cells Histone H3 (tri-methyl K27) marks repressed chromatin regions Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Regions of enriched signal in experiment MEL H3K27me3 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k09me3IggrabPk MEL H3K9m3 rab immortalized H3K9me3 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM003327 3327 GSM1003755 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k09me3IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL H3K9me3 IgG-rab Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k09me3Dm2p5dStdPk MEL H3K9m3 DMSO immortalized H3K9me3 MEL std ChipSeq ENCODE Jul 2012 Freeze 2012-07-31 2013-05-01 wgEncodeEM003333 3333 GSM1003748 Snyder Stanford-m exp M Unknown wgEncodeSydhHistMelH3k09me3Dm2p5dStdPk DMSO_2.0pct Peaks Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Regions of enriched signal in experiment MEL H3K9me3 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k04me3IggyalePk MEL H3K4m3 Y immortalized H3K4me3 MEL IgG-Yale ChipSeq ENCODE Mar 2012 Freeze 2011-07-19 2010-04-22 2011-01-22 wgEncodeEM002002 2002 GSM798324 Snyder Yale-m exp M Unknown wgEncodeSydhHistMelH3k04me3IggyalePk None Peaks Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Leukemia (K562 analog) Input signal from Mouse IgG ChIP-seq prepared at Yale Chromatin IP Sequencing Snyder Weissman - Yale University Male Unknown strain origin Regions of enriched signal in experiment MEL H3K4me3 IgG-Yale Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k04me3IggrabPk MEL H3K4m3 rab immortalized H3K4me3 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM003325 3325 GSM1003753 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k04me3IggrabPk None Peaks Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL H3K4me3 IgG-rab Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k04me3Dm2p5dIggyalePk MEL H3K4m3 DMSO Y immortalized H3K4me3 MEL IgG-Yale ChipSeq ENCODE Mar 2012 Freeze 2011-04-20 2012-01-20 wgEncodeEM002005 2005 GSM798328 Snyder Yale-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k04me3Dm2p5dIggyalePk DMSO_2.0pct Peaks Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Leukemia (K562 analog) Input signal from Mouse IgG ChIP-seq prepared at Yale Chromatin IP Sequencing Snyder Weissman - Yale University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Regions of enriched signal in experiment MEL H3K4me3 DMSO 2% IgG-Yale Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k04me3Dm2p5dStdPk MEL H3K4m3 DMSO immortalized H3K4me3 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM003326 3326 GSM1003754 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k04me3Dm2p5dStdPk DMSO_2.0pct Peaks Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Regions of enriched signal in experiment MEL H3K4me3 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k04me1IggrabPk MEL H3K4m1 rab immortalized H3K4me1 MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-05-10 2013-02-10 wgEncodeEM003330 3330 GSM1003744 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k04me1IggrabPk None Peaks Immortal cells Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL H3K4me1 IgG-rab Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistMelH3k04me1Dm2p5dStdPk MEL H3K4m1 DMSO immortalized H3K4me1 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEM003329 3329 GSM1003757 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhHistMelH3k04me1Dm2p5dStdPk DMSO_2.0pct Peaks Immortal cells Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Regions of enriched signal in experiment MEL H3K4me1 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistEse14H3k09me3StdPk ES-E14 H3K9m3 E0 H3K9me3 ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM003323 3323 GSM1003751 Snyder Stanford-m PeakSeq1.0 exp M 129/Ola wgEncodeSydhHistEse14H3k09me3StdPk None Peaks Embryonic day 0 (stem cell) 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. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistEse14H3k04me3StdPk ES-E14 H3K4m3 E0 H3K4me3 ES-E14 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEM003328 3328 GSM1003756 Snyder Stanford-m PeakSeq1.0 exp M 129/Ola wgEncodeSydhHistEse14H3k04me3StdPk None Peaks Embryonic day 0 (stem cell) Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistEse14H3k04me1StdPk ES-E14 H3K4m1 E0 H3K4me1 ES-E14 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM003322 3322 GSM1003750 Snyder Stanford-m PeakSeq1.0 exp M 129/Ola wgEncodeSydhHistEse14H3k04me1StdPk None Peaks Embryonic day 0 (stem cell) Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhHistCh12H3k4me3IggyalePk CH12 H3K4m3 Y immortalized H3K4me3 CH12 IgG-Yale ChipSeq ENCODE Mar 2012 Freeze 2010-05-12 2011-02-12 wgEncodeEM002004 2004 GSM798327 Snyder Yale-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhHistCh12H3k4me3IggyalePk None Peaks Immortal cells Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated. B-cell lymphoma (GM12878 analog) Input signal from Mouse IgG ChIP-seq prepared at Yale Chromatin IP Sequencing Snyder Weissman - Yale University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 H3K4me3 IgG-Yale Histone Mods by ChIP-seq Peaks from ENCODE/SYDH Expression and Regulation 
wgEncodeSydhRnaSeq Stan/Yale RNA-seq GSE39619 RNA-seq from ENCODE/Stanford/Yale Expression and Regulation Description This track shows enrichment of RNA sequence tags mapped to the mouse genome generated by high throughput sequencing (RNA-Seq). Double stranded cDNA was synthesized from enriched RNA that was obtained after depletion of ribosomal RNA. Pieces of cDNA, 300-350 nucleotides in length, were PCR amplified, adapter ligated, and sequenced on an Illumina HiSeq sequencer. Display Conventions and Configuration 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. 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. Methods Cells were grown according to the approved ENCODE cell culture protocols. Total RNA was extracted using RNeasy Mini Kit (74104, Aiagen), following the manufacturer's protocol. Ribosomal RNA was removed from total RNA using the Ribo-Zero Gold Kits (MRZG126, Epicentre). Double-stranded cDNA synthesis was performed on the rRNA depleted RNA using random primers and the SuperScript double-stranded cDNA synthesis kit (11917-010, Life Tech). After first strand cDNA synthesis, NucAway Spin Column (Ambion cat. 100070-30) was used to remove dNTPs. In the second strand cDNA synthesis reaction, dTTP in the dNTP mix was substituted with dUTP. After end repair and addition of 'A' base to 3' end, illumina paired-end adapter was ligated to Double-stranded cDNA library. After gel size selection of adapter ligated cDNA (300-350), Uracil-N-Glycosylase (UNG: Applied Biosystems) was used to digest the second strand cDNA (Parkhomchuk et al. , 2009). PCR amplified adapter ligated cDNA was sequenced using Illumina HiSeq. Sequence reads of 2x101 nt long with 0-2 mismatches were mapped to the mouse genome (version mm9) using the BWA aligner, version 0.5.7. The signal height corresponds to the number of overlapping fragments at each nucleotide position in the genome. Release Notes This is Release 2 (August 12) of this track. The bigwig file for the MEL cell, replicate 2 with no treatment, was corrupt and has been replaced. Credits These data were generated and analyzed by the labs of Michael Snyder. &nbsp;Contact: Philip Cayting. 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. PMID: 19620212; PMC: PMC2764448 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. 
wgEncodeSydhRnaSeqViewAlignments Alignments RNA-seq from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhRnaSeqMelRibozerogR2x101dAlnRep2 MEL Aln 2 immortalized MEL RnaSeq ENCODE Jul 2012 Freeze 2012-05-01 2013-02-01 wgEncodeEM001999 1999 Snyder Stanford-m cell mm9 2x101D 2 riboZeroGold Illumina_HiSeq_2000 M Unknown wgEncodeSydhRnaSeqMelRibozerogR2x101dAlnRep2 None Alignments Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Snyder Snyder - Stanford University Whole cell Paired 101 nt directed reads Ribo-Zero&trade; Gold Kits, removes both cytoplasmic (nuclear-encoded) rRNA and mitochondrial rRNA from 1 to 5 &micro;g of human, mouse, or rat total RNA Illumina HiSeq 2000 Male Unknown strain origin Shows individual reads mapped to the genome and indicates where bases may mismatch MEL RNA-seq Alignments Rep 2 from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhRnaSeqMelRibozerogR2x101dAlnRep1 MEL Aln 1 immortalized MEL RnaSeq ENCODE Jul 2012 Freeze 2012-05-01 2013-02-01 wgEncodeEM001999 1999 Snyder Stanford-m cell mm9 2x101D 1 riboZeroGold Illumina_HiSeq_2000 M Unknown wgEncodeSydhRnaSeqMelRibozerogR2x101dAlnRep1 None Alignments Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Snyder Snyder - Stanford University Whole cell Paired 101 nt directed reads Ribo-Zero&trade; Gold Kits, removes both cytoplasmic (nuclear-encoded) rRNA and mitochondrial rRNA from 1 to 5 &micro;g of human, mouse, or rat total RNA Illumina HiSeq 2000 Male Unknown strain origin Shows individual reads mapped to the genome and indicates where bases may mismatch MEL RNA-seq Alignments Rep 1 from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhRnaSeqMelDm2p5dRibozerogR2x101dAlnRep2 MEL DMSO Aln 2 immortalized MEL RnaSeq ENCODE Jul 2012 Freeze 2012-04-19 2013-01-19 wgEncodeEM001998 1998 Snyder Stanford-m cell mm9 2x101D 2 riboZeroGold Illumina_HiSeq_2000 M Unknown wgEncodeSydhRnaSeqMelDm2p5dRibozerogR2x101dAlnRep2 DMSO_2.0pct Alignments Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Snyder Snyder - Stanford University Whole cell Paired 101 nt directed reads Ribo-Zero&trade; Gold Kits, removes both cytoplasmic (nuclear-encoded) rRNA and mitochondrial rRNA from 1 to 5 &micro;g of human, mouse, or rat total RNA Illumina HiSeq 2000 Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Shows individual reads mapped to the genome and indicates where bases may mismatch MEL DMSO 2.0% RNA-seq Alignments Rep 2 from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhRnaSeqMelDm2p5dRibozerogR2x101dAlnRep1 MEL DMSO Aln 1 immortalized MEL RnaSeq ENCODE Jul 2012 Freeze 2012-04-19 2013-01-19 wgEncodeEM001998 1998 Snyder Stanford-m cell mm9 2x101D 1 riboZeroGold Illumina_HiSeq_2000 M Unknown wgEncodeSydhRnaSeqMelDm2p5dRibozerogR2x101dAlnRep1 DMSO_2.0pct Alignments Immortal cells Leukemia (K562 analog) Sequencing analysis of RNA expression Snyder Snyder - Stanford University Whole cell Paired 101 nt directed reads Ribo-Zero&trade; Gold Kits, removes both cytoplasmic (nuclear-encoded) rRNA and mitochondrial rRNA from 1 to 5 &micro;g of human, mouse, or rat total RNA Illumina HiSeq 2000 Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Shows individual reads mapped to the genome and indicates where bases may mismatch MEL DMSO 2.0% RNA-seq Alignments Rep 1 from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhRnaSeqEse14RibozerogR2x101dAlnRep2 ES-E14 Aln 2 E0 ES-E14 RnaSeq ENCODE Jul 2012 Freeze 2012-04-19 2013-01-19 wgEncodeEM002899 2899 Snyder Stanford-m cell mm9 2x101D 2 riboZeroGold Illumina_HiSeq_2000 M 129/Ola wgEncodeSydhRnaSeqEse14RibozerogR2x101dAlnRep2 None Alignments Embryonic day 0 (stem cell) mouse embryonic stem cell line E14 Sequencing analysis of RNA expression Snyder Snyder - Stanford University Whole cell Paired 101 nt directed reads Ribo-Zero&trade; Gold Kits, removes both cytoplasmic (nuclear-encoded) rRNA and mitochondrial rRNA from 1 to 5 &micro;g of human, mouse, or rat total RNA Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Shows individual reads mapped to the genome and indicates where bases may mismatch ES-E14 RNA-seq Alignments Rep 2 from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhRnaSeqEse14RibozerogR2x101dAlnRep1 ES-E14 Aln 1 E0 ES-E14 RnaSeq ENCODE Jul 2012 Freeze 2012-04-19 2013-01-19 wgEncodeEM002899 2899 Snyder Stanford-m cell mm9 2x101D 1 riboZeroGold Illumina_HiSeq_2000 M 129/Ola wgEncodeSydhRnaSeqEse14RibozerogR2x101dAlnRep1 None Alignments Embryonic day 0 (stem cell) mouse embryonic stem cell line E14 Sequencing analysis of RNA expression Snyder Snyder - Stanford University Whole cell Paired 101 nt directed reads Ribo-Zero&trade; Gold Kits, removes both cytoplasmic (nuclear-encoded) rRNA and mitochondrial rRNA from 1 to 5 &micro;g of human, mouse, or rat total RNA Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Shows individual reads mapped to the genome and indicates where bases may mismatch ES-E14 RNA-seq Alignments Rep 1 from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhRnaSeqCh12RibozerogR2x101dAlnRep2 CH12 Aln 2 immortalized CH12 RnaSeq ENCODE Jul 2012 Freeze 2012-04-19 2013-01-19 wgEncodeEM002000 2000 Snyder Stanford-m cell mm9 2x101D 2 riboZeroGold Illumina_HiSeq_2000 F B10.H-2aH-4bp/Wts wgEncodeSydhRnaSeqCh12RibozerogR2x101dAlnRep2 None Alignments Immortal cells B-cell lymphoma (GM12878 analog) Sequencing analysis of RNA expression Snyder Snyder - Stanford University Whole cell Paired 101 nt directed reads Ribo-Zero&trade; Gold Kits, removes both cytoplasmic (nuclear-encoded) rRNA and mitochondrial rRNA from 1 to 5 &micro;g of human, mouse, or rat total RNA Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Shows individual reads mapped to the genome and indicates where bases may mismatch CH12 RNA-seq Alignments Rep 2 from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhRnaSeqCh12RibozerogR2x101dAlnRep1 CH12 Aln 1 immortalized CH12 RnaSeq ENCODE Jul 2012 Freeze 2012-04-19 2013-01-19 wgEncodeEM002000 2000 Snyder Stanford-m cell mm9 2x101D 1 riboZeroGold Illumina_HiSeq_2000 F B10.H-2aH-4bp/Wts wgEncodeSydhRnaSeqCh12RibozerogR2x101dAlnRep1 None Alignments Immortal cells B-cell lymphoma (GM12878 analog) Sequencing analysis of RNA expression Snyder Snyder - Stanford University Whole cell Paired 101 nt directed reads Ribo-Zero&trade; Gold Kits, removes both cytoplasmic (nuclear-encoded) rRNA and mitochondrial rRNA from 1 to 5 &micro;g of human, mouse, or rat total RNA Illumina HiSeq 2000 Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Shows individual reads mapped to the genome and indicates where bases may mismatch CH12 RNA-seq Alignments Rep 1 from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbs Stan/Yale TFBS GSE36030 Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale Expression and 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). Each experiment is associated with an input signal, which represents the control condition where immunoprecipitation with non-specific immunoglobulin was performed in the same cell type. 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, as identified by the PeakSeq algorithm (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. This track contains the following views: Peaks Regions of signal enrichment based on processed data (normalized data from pooled replicates). Intensity is represented in grayscale, the darker shading shows higher intensity (a solid vertical line in the peak region represents the the point with the highest signal). 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. For details on the chromatin immunoprecipitation protocol used, see (Euskirchen et al., 2007), (Rozowsky et al., 2009) and (Auerbach 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 bps) 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. Reads were pooled from all submitted replicates to generate the Peak and Signal files. Per-replicate aligments and sequences are available for download at downloads page. For each 1 Mb segment of each chromosome, a peak height threshold was determined by requiring a false discovery rate &lt;= 0.01 when comparing the number of peaks above said threshold to the number of peaks 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 &le; 0.01 are considered to be significantly enriched compared to the input DNA control. Release Notes This is Release 4 (August 2012). It contains a total of 88 ChIP-seq experiments on transcriptions factor binding with the addition of 22 new experiments including 12 new antibodies. Previous versions of files are available for download from the FTP site. Credits These data were generated and analyzed by the labs of Michael Snyder at Stanford University and Sherman Weissman at Yale University. Contact: Philip Cayting. References Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefran&#231;ois P, Struhl K, Gerstein M, Snyder M. Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14926-31. 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. 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. 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. 
wgEncodeSydhTfbsViewSig Snal Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelCmycIggrabSig MEL c-Myc immortalized c-Myc MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001951 1951 GSM912934 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelCmycIggrabSig None Signal Immortal cells transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL c-Myc TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelCmybsc7874IggrabSig MEL c-Myb immortalized c-Myb_(SC-7874) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-10-27 2011-07-27 wgEncodeEM001967 1967 GSM912903 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelCmybsc7874IggrabSig None Signal Immortal cells Transcriptional activator; DNA-binding protein that specifically recognize the sequence 5'-YAAC[GT]G-3'. Plays an important role in the control of proliferation and differentiation of hematopoietic progenitor cells. Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL c-Myb TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelInputStdSig MEL Input immortalized Input MEL std ChipSeq ENCODE Mar 2012 Freeze 2011-04-29 2012-01-28 wgEncodeEM001982 1982 GSM912916 Snyder Stanford-m PeakSeq1.0 input M Unknown wgEncodeSydhTfbsMelInputStdSig None Signal Immortal cells Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL Standard Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelInputDm2p5dStdSig MEL Input D immortalized Input MEL std ChipSeq ENCODE Mar 2012 Freeze 2011-04-29 2012-01-29 wgEncodeEM001983 1983 GSM912897 Snyder Yale-m PeakSeq1.0 input M Unknown wgEncodeSydhTfbsMelInputDm2p5dStdSig DMSO_2.0pct Signal Immortal cells Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Weissman - Yale University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL Standard Input DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelInputDm2p5dStdSigV2 MEL Input D immortalized Input MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002791 2791 GSM1003812 Snyder Stanford-m PeakSeq1.0 input M Unknown wgEncodeSydhTfbsMelInputDm2p5dStdSigV2 DMSO_2.0pct Signal Immortal cells Leukemia (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL Input DMSO 2% ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelInputDm2p5dIggyaleSig MEL IgG-Y D immortalized Input MEL IgG-Yale ChipSeq ENCODE Mar 2012 Freeze 2010-07-09 2011-04-09 wgEncodeEM001963 1963 GSM913032 Snyder Yale-m PeakSeq1.0 input M Unknown wgEncodeSydhTfbsMelInputDm2p5dIggyaleSig DMSO_2.0pct Signal Immortal cells Leukemia (K562 analog) Input signal from Mouse IgG ChIP-seq prepared at Yale Chromatin IP Sequencing Snyder Weissman - Yale University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL IgG-Yale Input DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelInputIggratSig MEL IgG-rat immortalized Input MEL IgG-rat ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001948 1948 GSM912894 Snyder Stanford-m PeakSeq1.0 input M Unknown wgEncodeSydhTfbsMelInputIggratSig None Signal Immortal cells Leukemia (K562 analog) Input signal from Normal Rat IgG ChIP-seq Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL IgG-rat Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelInputDm2p5dIggratSig MEL Input D immortalized Input MEL IgG-rat ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEM002782 2782 GSM1003787 Snyder Stanford-m PeakSeq1.0 input M Unknown wgEncodeSydhTfbsMelInputDm2p5dIggratSig DMSO_2.0pct Signal Immortal cells Leukemia (K562 analog) Input signal from Normal Rat IgG ChIP-seq Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL DMSO 2% Input IgG-rat TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelInputIggrabSig MEL IgG-rab immortalized Input MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001947 1947 GSM912905 Snyder Stanford-m PeakSeq1.0 input M Unknown wgEncodeSydhTfbsMelInputIggrabSig None Signal Immortal cells Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL IgG-rab Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelInputIggmusSig MEL IgG-mus immortalized Input MEL IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001946 1946 GSM912904 Snyder Stanford-m PeakSeq1.0 input M Unknown wgEncodeSydhTfbsMelInputIggmusSig None Signal Immortal cells Leukemia (K562 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL IgG-mus Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelZnfmizdcp1ab65767IggrabSig MEL ZNF-MIZD S immortalized ZNF-MIZD-CP1_(ab65767) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003354 3354 GSM1003798 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelZnfmizdcp1ab65767IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL ZNF-MIZD-CP1 (ab65767) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelZnf384hpa004051IggrabSig MEL ZNF384 S immortalized ZNF384_(HPA004051) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003355 3355 GSM1003797 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelZnf384hpa004051IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL ZNF384 (HPA004051) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelZkscan1hpa006672IggrabSig MEL ZKSCAN1_H immortalized ZKSCAN1_(HPA006672) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002793 2793 GSM1003779 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelZkscan1hpa006672IggrabSig None Signal Immortal cells 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. Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL ZKSCAN1 (HPA006672) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelZc3h11anb10074650IggrabSig MEL ZC3H11A S immortalized ZC3H11A_(NB100-74650) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003353 3353 GSM1003776 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelZc3h11anb10074650IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL ZC3H11A (NB100-74650) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelUsf2IggrabSig MEL USF2 Ig_r immortalized USF2 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-22 2012-06-21 wgEncodeEM002780 2780 GSM1003785 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelUsf2IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL USF2 IgG-rab TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelUsf2IggmusSig MEL USF2 Ig_m immortalized USF2 MEL IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001960 1960 GSM912892 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelUsf2IggmusSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL USF2 IgG_mus TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelUbfsc13125IggmusSig MEL UBF S immortalized UBF_(sc-13125) MEL IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003342 3342 GSM1003788 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelUbfsc13125IggmusSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL UBF (sc-13125) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelTbpIggmusSig MEL TBP immortalized TBP MEL IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001950 1950 GSM912913 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelTbpIggmusSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL TBP TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelSmc3ab9263IggrabSig MEL SMC3 immortalized SMC3_(ab9263) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-20 2012-01-20 wgEncodeEM001978 1978 GSM912923 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelSmc3ab9263IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL SMC3 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelSin3anb6001263IggrabSig MEL SIN3A_N immortalized SIN3A_(NB600-1263) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002785 2785 GSM1003780 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelSin3anb6001263IggrabSig None Signal Immortal cells 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). Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL SIN3A (NB600-1263) IgG-rab TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelRad21IggrabSig MEL Rad21 immortalized Rad21 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-10-20 2011-07-20 wgEncodeEM001966 1966 GSM912935 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelRad21IggrabSig None Signal Immortal cells Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL Rad21 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelRad21Dm2p5dIggrabSig MEL Rad21 D immortalized Rad21 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-10-20 2011-07-20 wgEncodeEM001965 1965 GSM912933 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelRad21Dm2p5dIggrabSig DMSO_2.0pct Signal Immortal cells Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL Rad21 DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelPol2s2IggrabSig MEL Pol2S2 immortalized Pol2(phosphoS2) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEM001974 1974 GSM912927 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelPol2s2IggrabSig None Signal Immortal cells RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL Pol2(phosphoS2) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelPol2IggmusSig MEL Pol2 immortalized Pol2 MEL IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001949 1949 GSM912895 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelPol2IggmusSig None Signal Immortal cells RNA Polymerase II Leukemia (K562 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL Pol2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelPol2Dm2p5dIggrabSig MEL Pol2 D immortalized Pol2 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-22 2012-06-21 wgEncodeEM002779 2779 GSM1003775 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelPol2Dm2p5dIggrabSig DMSO_2.0pct Signal Immortal cells RNA Polymerase II Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL Pol2 DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelP300sc584IggrabSig MEL p300 SC-584 immortalized p300_(SC-584) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001961 1961 GSM912893 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelP300sc584IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL p300 (SC-584) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelP300IggrabSigV2 MEL p300 immortalized p300 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-12-10 2011-09-10 wgEncodeEM001969 1969 GSM912921 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelP300IggrabSigV2 None Signal Immortal cells EP300(c-20) Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL p300 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelNrf2IggrabSig MEL Nrf2 S immortalized Nrf2 MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003341 3341 GSM1003791 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelNrf2IggrabSig None Signal Immortal cells Epitope corresponding to amino acids 1-180 mapping at the N-terminus of GABP-&#945 of human origin Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL Nrf2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelNelfeIggrabSig MEL NELFe immortalized NELFe MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-10-20 2011-07-20 wgEncodeEM001964 1964 GSM912932 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelNelfeIggrabSig None Signal Immortal cells NELF-E (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation. Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL NELFe TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelMxi1af4185IggrabSig MEL Mxi1 immortalized Mxi1_(AF4185) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEM001973 1973 GSM912928 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelMxi1af4185IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL Mxi1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelMazab85725IggrabSig MEL MAZ S immortalized MAZ_(ab85725) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003340 3340 GSM1003790 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelMazab85725IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL MAZ (ab85725) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelMaxIggrabSig MEL Max immortalized Max MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001959 1959 GSM912919 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelMaxIggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL Max TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelMafkab50322IggrabSig MEL MafK_a immortalized MafK_(ab50322) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEM001981 1981 GSM912899 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelMafkab50322IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL MafK (ab50322) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelMafkDm2p5dStdSig MEL MafK_a D immortalized MafK_(ab50322) MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002792 2792 GSM1003806 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelMafkDm2p5dStdSig DMSO_2.0pct Signal Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL MafK (ab50322) DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelJundIggrabSig MEL JunD immortalized JunD MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-05-11 2011-02-11 wgEncodeEM001952 1952 GSM912915 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelJundIggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL JunD TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelHcfc1nb10068209IggrabSig MEL HCFC1 S immortalized HCFC1_(NB100-68209) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003352 3352 GSM1003778 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelHcfc1nb10068209IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL HCFC1 (NB100-68209) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelGcn5IggrabSig MEL GCN5 S immortalized GCN5 MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003339 3339 GSM1003804 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelGcn5IggrabSig None Signal Immortal cells 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 Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL GCN5 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelGata1IggratSig MEL GATA-1 immortalized GATA-1 MEL IgG-rat ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001945 1945 GSM912907 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelGata1IggratSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rat IgG ChIP-seq Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL GATA-1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelGata1Dm2p5dStdSig MEL GATA-1 D immortalized GATA-1 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002790 2790 GSM1003808 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelGata1Dm2p5dStdSig DMSO_2.0pct Signal Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL GATA-1 DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelEts1IggrabSig MEL ETS1 immortalized ETS1 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002789 2789 GSM1003777 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelEts1IggrabSig None Signal Immortal cells ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL ETS1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelE2f4IggrabSig MEL E2F4 immortalized E2F4 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-05-12 2011-02-12 wgEncodeEM001953 1953 GSM912914 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelE2f4IggrabSig None Signal Immortal cells mapping at the C-terminus of E2F4 of human origin Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL E2F4 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelCtcfsc15914IggrabSig MEL CTCF immortalized CTCF_(SC-15914) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-12-10 2011-09-10 wgEncodeEM001968 1968 GSM912896 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelCtcfsc15914IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL CTCF TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelCtcfbDm2p5dStdSig MEL CTCF_S D immortalized CTCF_(SC-15914) MEL std ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEM002781 2781 GSM1003784 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelCtcfbDm2p5dStdSig DMSO_2.0pct Signal Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Signal MEL CTCF (SC-15914) DMSO 2% ChIP-seq TFBS Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelCorestsc30189IggrabSig MEL COREST S immortalized COREST_(sc-30189) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEM003343 3343 GSM1003789 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelCorestsc30189IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL COREST (sc-30189) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelChd2ab68301IggrabSig MEL CHD2 immortalized CHD2_(AB68301) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEM001972 1972 GSM912929 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelChd2ab68301IggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL CHD2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelChd1nb10060411IggrabSig MEL CHD1 S immortalized CHD1_(NB100-60411) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003338 3338 GSM1003805 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelChd1nb10060411IggrabSig None Signal Immortal cells 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 Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL CHD1 (NB100-60411) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelBhlhe40cIggrabSig MEL BHLHE40 S immortalized BHLHE40_(NB100-1800) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEM003344 3344 GSM1003794 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelBhlhe40cIggrabSig None Signal Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Signal MEL BHLHE40 (NB100-1800) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsEse14InputStdSig ES-E14 Input E0 Input ES-E14 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002788 2788 GSM1003811 Snyder Stanford-m PeakSeq1.0 input M 129/Ola wgEncodeSydhTfbsEse14InputStdSig None Signal Embryonic day 0 (stem cell) mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsEse14Znf384hpa004051StdSig ES-E14 ZNF384 S E0 ZNF384_(HPA004051) ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003351 3351 GSM1003807 Snyder Stanford-m exp M 129/Ola wgEncodeSydhTfbsEse14Znf384hpa004051StdSig None Signal Embryonic day 0 (stem cell) 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. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 ZNF384 (HPA004051) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsEse14Zc3h11anb10074650StdSig ES-E14 ZC3H11A S E0 ZC3H11A_(NB100-74650) ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003350 3350 GSM1003810 Snyder Stanford-m exp M 129/Ola wgEncodeSydhTfbsEse14Zc3h11anb10074650StdSig None Signal Embryonic day 0 (stem cell) 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. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 ZC3H11A (NB100-74650) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsEse14MafkStdSig ES-E14 MafK_a E0 MafK_(ab50322) ES-E14 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEM002794 2794 GSM1003809 Snyder Stanford-m PeakSeq1.0 exp M 129/Ola wgEncodeSydhTfbsEse14MafkStdSig None Signal Embryonic day 0 (stem cell) 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. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 MafK (ab50322) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsEse14Hcfc1nb10068209StdSig ES-E14 HCFC1 S E0 HCFC1_(NB100-68209) ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003349 3349 GSM1003799 Snyder Stanford-m exp M 129/Ola wgEncodeSydhTfbsEse14Hcfc1nb10068209StdSig None Signal Embryonic day 0 (stem cell) The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 HCFC1 (NB100-68209) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12CmycIggrabSig CH12 c-Myc immortalized c-Myc CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001944 1944 GSM912906 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12CmycIggrabSig None Signal Immortal cells transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 c-Myc TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12CjunIggrabSig CH12 c-Jun immortalized c-Jun CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001943 1943 GSM912901 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12CjunIggrabSig None Signal Immortal cells Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 c-Jun TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12InputIggrabSig CH12 IgG-rab immortalized Input CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001939 1939 GSM912917 Snyder Stanford-m PeakSeq1.0 input F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12InputIggrabSig None Signal Immortal cells B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 IgG-rab Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12InputIggmusSig CH12 IgG-mus immortalized Input CH12 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001938 1938 GSM912918 Snyder Stanford-m PeakSeq1.0 input F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12InputIggmusSig None Signal Immortal cells B-cell lymphoma (GM12878 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 IgG-mus Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Znfmizdcp1ab65767IggrabSig CH12 ZNF-MIZD S immortalized ZNF-MIZD-CP1_(ab65767) CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003347 3347 GSM1003793 Snyder Stanford-m exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Znfmizdcp1ab65767IggrabSig None Signal Immortal cells 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. B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 ZNF-MIZD-CP1 (ab65767) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Znf384hpa004051IggrabSig CH12 ZNF384 S immortalized ZNF384_(HPA004051) CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003348 3348 GSM1003796 Snyder Stanford-m exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Znf384hpa004051IggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 ZNF384 (HPA004051) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Zkscan1hpa006672IggrabSig CH12 ZKSCAN1_H immortalized ZKSCAN1_(HPA006672) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002787 2787 GSM1003782 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Zkscan1hpa006672IggrabSig None Signal Immortal cells 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. B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 ZKSCAN1 (HPA006672) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Zc3h11anb10074650IggrabSig CH12 ZC3H11A S immortalized ZC3H11A_(NB100-74650) CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003346 3346 GSM1003792 Snyder Stanford-m exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Zc3h11anb10074650IggrabSig None Signal Immortal cells 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. B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 ZC3H11A (NB100-74650) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Usf2IggmusSig CH12 USF2 immortalized USF2 CH12 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001957 1957 GSM912910 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Usf2IggmusSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 USF2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Ubfsc13125IggrabSig CH12 UBF_s immortalized UBF_(sc-13125) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002786 2786 GSM1003783 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Ubfsc13125IggrabSig None Signal Immortal cells 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 B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 UBF (sc-13125) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12TbpIggmusSig CH12 TBP immortalized TBP CH12 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001942 1942 GSM912900 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12TbpIggmusSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 TBP TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Smc3ab9263IggrabSig CH12 SMC3 immortalized SMC3_(ab9263) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEM001971 1971 GSM912930 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Smc3ab9263IggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 SMC3 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Sin3anb6001263IggrabSig CH12 SIN3A_N immortalized SIN3A_(NB600-1263) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002784 2784 GSM1003781 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Sin3anb6001263IggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 SIN3A (NB600-1263) IgG-rab TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Rad21IggrabSig CH12 Rad21 immortalized Rad21 CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001956 1956 GSM912911 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Rad21IggrabSig None Signal Immortal cells Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 Rad21 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Pol2s2IggrabSig CH12 Pol2S2 immortalized Pol2(phosphoS2) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEM001970 1970 GSM912931 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Pol2s2IggrabSig None Signal Immortal cells RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 Pol2(phosphoS2) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Pol2IggmusSig CH12 Pol2 immortalized Pol2 CH12 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001941 1941 GSM912891 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Pol2IggmusSig None Signal Immortal cells RNA Polymerase II B-cell lymphoma (GM12878 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 Pol2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12P300sc584IggrabSig CH12 p300 SC-584 immortalized p300_(SC-584) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001958 1958 GSM912920 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12P300sc584IggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 p300 (SC-584) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Nrf2IggrabSig CH12 Nrf2 S immortalized Nrf2 CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003337 3337 GSM1003800 Snyder Stanford-m exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Nrf2IggrabSig None Signal Immortal cells Epitope corresponding to amino acids 1-180 mapping at the N-terminus of GABP-&#945 of human origin B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 Nrf2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12NelfeIggrabSig CH12 NELFe immortalized NELFe CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-20 2012-01-20 wgEncodeEM001977 1977 GSM912924 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12NelfeIggrabSig None Signal Immortal cells NELF-E (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation. B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 NELFe TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Mxi1af4185IggrabSig CH12 Mxi1 immortalized Mxi1_(AF4185) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-15 2011-12-14 wgEncodeEM001976 1976 GSM912925 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Mxi1af4185IggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 Mxi1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Mazab85725IggrabSig CH12 MAZ S immortalized MAZ_(ab85725) CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003336 3336 GSM1003801 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Mazab85725IggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 MAZ (ab85725) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12MaxIggrabSig CH12 Max immortalized Max CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001955 1955 GSM912908 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12MaxIggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 Max TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Mafkab50322IggrabSig CH12 MafK_a immortalized MafK_(ab50322) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEM001980 1980 GSM912898 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Mafkab50322IggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 MafK (ab50322) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12JundIggrabSig CH12 JunD immortalized JunD CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001940 1940 GSM912902 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12JundIggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 JunD TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Hcfc1nb10068209IggrabSig CH12 HCFC1 S immortalized HCFC1_(NB100-68209) CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003345 3345 GSM1003795 Snyder Stanford-m exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Hcfc1nb10068209IggrabSig None Signal Immortal cells The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 HCFC1 (NB100-68209) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Gcn5IggrabSig CH12 GCN5 S immortalized GCN5 CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003335 3335 GSM1003802 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Gcn5IggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 GCN5 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Ets1IggrabSig CH12 ETS1 immortalized ETS1 CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-22 2012-06-21 wgEncodeEM002778 2778 GSM1003774 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Ets1IggrabSig None Signal Immortal cells ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 ETS1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12E2f4IggrabSig CH12 E2F4 immortalized E2F4 CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001937 1937 GSM912912 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12E2f4IggrabSig None Signal Immortal cells mapping at the C-terminus of E2F4 of human origin B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 E2F4 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12CtcfbIggrabSig CH12 CTCF immortalized CTCF_(SC-15914) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2010-07-08 2011-04-08 wgEncodeEM001954 1954 GSM912909 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12CtcfbIggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 CTCF TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Corestsc30189IggrabSig CH12 COREST_s immortalized COREST_(sc-30189) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM002783 2783 GSM1003786 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Corestsc30189IggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 COREST (sc30189) IgG-rab TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Chd2ab68301IggrabSig CH12 CHD2 immortalized CHD2_(AB68301) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-15 2011-12-14 wgEncodeEM001975 1975 GSM912926 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Chd2ab68301IggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 CHD2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Chd1nb10060411IggrabSig CH12 CHD1 S immortalized CHD1_(NB100-60411) CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003334 3334 GSM1003803 Snyder Stanford-m exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Chd1nb10060411IggrabSig None Signal Immortal cells 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 B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 CHD1 (NB100-60411) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Bhlhe40nb100IggrabSig CH12 BHLHE40 immortalized BHLHE40_(NB100-1800) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEM001979 1979 GSM912922 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Bhlhe40nb100IggrabSig None Signal Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 BHLHE40 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsViewPeaks Peaks Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelCmycIggrabPk MEL c-Myc immortalized c-Myc MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-07-19 2010-04-22 2011-01-22 wgEncodeEM001951 1951 GSM912934 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelCmycIggrabPk None Peaks Immortal cells transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL c-Myc TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelCmybsc7874IggrabPk MEL c-Myb immortalized c-Myb_(SC-7874) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-10-27 2011-07-27 wgEncodeEM001967 1967 GSM912903 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelCmybsc7874IggrabPk None Peaks Immortal cells Transcriptional activator; DNA-binding protein that specifically recognize the sequence 5'-YAAC[GT]G-3'. Plays an important role in the control of proliferation and differentiation of hematopoietic progenitor cells. Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL c-Myb TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelZnfmizdcp1ab65767IggrabPk MEL ZNF-MIZD P immortalized ZNF-MIZD-CP1_(ab65767) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003354 3354 GSM1003798 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelZnfmizdcp1ab65767IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL ZNF-MIZD-CP1 (ab65767) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelZnf384hpa004051IggrabPk MEL ZNF384 P immortalized ZNF384_(HPA004051) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003355 3355 GSM1003797 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelZnf384hpa004051IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL ZNF384 (HPA004051) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelZkscan1hpa006672IggrabPk MEL ZKSCAN1_H immortalized ZKSCAN1_(HPA006672) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002793 2793 GSM1003779 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelZkscan1hpa006672IggrabPk None Peaks Immortal cells 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. Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL ZKSCAN1 (HPA006672) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelZc3h11anb10074650IggrabPk MEL ZC3H11A P immortalized ZC3H11A_(NB100-74650) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003353 3353 GSM1003776 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelZc3h11anb10074650IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL ZC3H11A (NB100-74650) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelUsf2IggrabPk MEL USF2 immortalized USF2 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-22 2012-06-21 wgEncodeEM002780 2780 GSM1003785 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelUsf2IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL USF2 IgG-rab TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelUsf2IggmusPk MEL USF2 immortalized USF2 MEL IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001960 1960 GSM912892 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelUsf2IggmusPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL USF2 IgG-mus TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelUbfsc13125IggmusPk MEL UBF P immortalized UBF_(sc-13125) MEL IgG-mus ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003342 3342 GSM1003788 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelUbfsc13125IggmusPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL UBF (sc-13125) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelTbpIggmusPk MEL TBP immortalized TBP MEL IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-07-19 2010-04-22 2011-01-22 wgEncodeEM001950 1950 GSM912913 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelTbpIggmusPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL TBP TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelSmc3ab9263IggrabPk MEL SMC3 immortalized SMC3_(ab9263) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-20 2012-01-20 wgEncodeEM001978 1978 GSM912923 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelSmc3ab9263IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL SMC3 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelSin3anb6001263IggrabPk MEL SIN3A_N immortalized SIN3A_(NB600-1263) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002785 2785 GSM1003780 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelSin3anb6001263IggrabPk None Peaks Immortal cells 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). Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL SIN3A (NB600-1263) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelRad21IggrabPk MEL Rad21 immortalized Rad21 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-10-20 2011-07-20 wgEncodeEM001966 1966 GSM912935 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelRad21IggrabPk None Peaks Immortal cells Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL Rad21 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelRad21Dm2p5dIggrabPk MEL Rad21 D immortalized Rad21 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-03 2010-10-20 2011-07-20 wgEncodeEM001965 1965 GSM912933 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelRad21Dm2p5dIggrabPk DMSO_2.0pct Peaks Immortal cells Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Regions of enriched signal in experiment MEL Rad21 DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelPol2s2IggrabPk MEL Pol2S2 immortalized Pol2(phosphoS2) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEM001974 1974 GSM912927 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelPol2s2IggrabPk None Peaks Immortal cells RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL Pol2(phosphoS2) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelPol2IggmusPk MEL Pol2 immortalized Pol2 MEL IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001949 1949 GSM912895 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelPol2IggmusPk None Peaks Immortal cells RNA Polymerase II Leukemia (K562 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL Pol2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelPol2Dm2p5dIggrabPk MEL Pol2 D immortalized Pol2 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-22 2012-06-21 wgEncodeEM002779 2779 GSM1003775 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelPol2Dm2p5dIggrabPk DMSO_2.0pct Peaks Immortal cells RNA Polymerase II Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Regions of enriched signal in experiment MEL Pol2 DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelP300sc584IggrabPk MEL p300 SC-584 immortalized p300_(SC-584) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001961 1961 GSM912893 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelP300sc584IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL p300 (SC-584) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelP300IggrabPkV2 MEL p300 immortalized p300 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-12-10 2011-09-10 wgEncodeEM001969 1969 GSM912921 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelP300IggrabPkV2 None Peaks Immortal cells EP300(c-20) Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL p300 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelNrf2IggrabPk MEL Nrf2 P immortalized Nrf2 MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003341 3341 GSM1003791 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelNrf2IggrabPk None Peaks Immortal cells Epitope corresponding to amino acids 1-180 mapping at the N-terminus of GABP-&#945 of human origin Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL Nrf2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelNelfeIggrabPk MEL NELFe immortalized NELFe MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-10-20 2011-07-20 wgEncodeEM001964 1964 GSM912932 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelNelfeIggrabPk None Peaks Immortal cells NELF-E (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation. Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL NELFe TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelMxi1af4185IggrabPk MEL Mxi1 immortalized Mxi1_(AF4185) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEM001973 1973 GSM912928 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelMxi1af4185IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL Mxi1 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelMazab85725IggrabPk MEL MAZ P immortalized MAZ_(ab85725) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003340 3340 GSM1003790 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelMazab85725IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL MAZ (ab85725) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelMaxIggrabPk MEL Max immortalized Max MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001959 1959 GSM912919 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelMaxIggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL Max TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelMafkab50322IggrabPk MEL MafK_a immortalized MafK_(ab50322) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEM001981 1981 GSM912899 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelMafkab50322IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL MafK (ab50322) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelMafkDm2p5dStdPk MEL MafK_a immortalized MafK_(ab50322) MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002792 2792 GSM1003806 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelMafkDm2p5dStdPk DMSO_2.0pct Peaks Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Regions of enriched signal in experiment MEL MafK (ab50322) DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelJundIggrabPk MEL JunD immortalized JunD MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-05-11 2011-02-11 wgEncodeEM001952 1952 GSM912915 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelJundIggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL JunD TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelHcfc1nb10068209IggrabPk MEL HCFC1 P immortalized HCFC1_(NB100-68209) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003352 3352 GSM1003778 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelHcfc1nb10068209IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL HCFC1 (NB100-68209) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelGcn5IggrabPk MEL GCN5 P immortalized GCN5 MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003339 3339 GSM1003804 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelGcn5IggrabPk None Peaks Immortal cells 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 Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL GCN5 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelGata1IggratPk MEL GATA-1 immortalized GATA-1 MEL IgG-rat ChipSeq ENCODE Mar 2012 Freeze 2011-07-19 2010-04-22 2011-01-22 wgEncodeEM001945 1945 GSM912907 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelGata1IggratPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rat IgG ChIP-seq Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL GATA-1 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelGata1Dm2p5dStdPk MEL GATA-1 immortalized GATA-1 MEL std ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002790 2790 GSM1003808 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelGata1Dm2p5dStdPk DMSO_2.0pct Peaks Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Regions of enriched signal in experiment MEL GATA-1 DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelEts1IggrabPk MEL ETS1 immortalized ETS1 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002789 2789 GSM1003777 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelEts1IggrabPk None Peaks Immortal cells ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL ETS1 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelE2f4IggrabPk MEL E2F4 immortalized E2F4 MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-05-12 2011-02-12 wgEncodeEM001953 1953 GSM912914 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelE2f4IggrabPk None Peaks Immortal cells mapping at the C-terminus of E2F4 of human origin Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL E2F4 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelCtcfbIggrabPk MEL CTCF immortalized CTCF_(SC-15914) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-07-19 2010-12-10 2011-09-10 wgEncodeEM001968 1968 GSM912896 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelCtcfbIggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL CTCF TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelCtcfbDm2p5dStdPk MEL CTCF_S immortalized CTCF_(SC-15914) MEL std ChipSeq ENCODE Mar 2012 Freeze 2011-09-29 2012-06-28 wgEncodeEM002781 2781 GSM1003784 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelCtcfbDm2p5dStdPk DMSO_2.0pct Peaks Immortal cells 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 (K562 analog) Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman) Regions of enriched signal in experiment MEL CTCF (SC-15914) DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelCorestsc30189IggrabPk MEL COREST P immortalized COREST_(sc-30189) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-01 2013-03-30 wgEncodeEM003343 3343 GSM1003789 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelCorestsc30189IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL COREST (sc-30189) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelChd2ab68301IggrabPk MEL CHD2 immortalized CHD2_(AB68301) MEL IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEM001972 1972 GSM912929 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelChd2ab68301IggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL CHD2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelChd1nb10060411IggrabPk MEL CHD1 P immortalized CHD1_(NB100-60411) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003338 3338 GSM1003805 Snyder Stanford-m exp M Unknown wgEncodeSydhTfbsMelChd1nb10060411IggrabPk None Peaks Immortal cells 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 Leukemia (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL CHD1 (NB100-60411) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsMelBhlhe40cIggrabPk MEL BHLHE40 P immortalized BHLHE40_(NB100-1800) MEL IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-07-19 2013-04-19 wgEncodeEM003344 3344 GSM1003794 Snyder Stanford-m PeakSeq1.0 exp M Unknown wgEncodeSydhTfbsMelBhlhe40cIggrabPk None Peaks Immortal cells 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 (K562 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Male Unknown strain origin Regions of enriched signal in experiment MEL BHLHE40 (NB100-1800) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsEse14Znf384hpa004051StdPk ES-E14 ZNF384 P E0 ZNF384_(HPA004051) ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003351 3351 GSM1003807 Snyder Stanford-m exp M 129/Ola wgEncodeSydhTfbsEse14Znf384hpa004051StdPk None Peaks Embryonic day 0 (stem cell) 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. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 ZNF384 (HPA004051) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsEse14Zc3h11anb10074650StdPk ES-E14 ZC3H11A P E0 ZC3H11A_(NB100-74650) ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003350 3350 GSM1003810 Snyder Stanford-m exp M 129/Ola wgEncodeSydhTfbsEse14Zc3h11anb10074650StdPk None Peaks Embryonic day 0 (stem cell) 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. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 ZC3H11A (NB100-74650) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsEse14MafkStdPk ES-E14 MafK_a E0 MafK_(ab50322) ES-E14 std ChipSeq ENCODE Mar 2012 Freeze 2012-03-30 2012-12-29 wgEncodeEM002794 2794 GSM1003809 Snyder Stanford-m PeakSeq1.0 exp M 129/Ola wgEncodeSydhTfbsEse14MafkStdPk None Peaks Embryonic day 0 (stem cell) 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. mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 MafK (ab50322) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsEse14Hcfc1nb10068209StdPk ES-E14 HCFC1 P E0 HCFC1_(NB100-68209) ES-E14 std ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003349 3349 GSM1003799 Snyder Stanford-m exp M 129/Ola wgEncodeSydhTfbsEse14Hcfc1nb10068209StdPk None Peaks Embryonic day 0 (stem cell) The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). mouse embryonic stem cell line E14 Standard input signal for most experiments. Chromatin IP Sequencing Snyder Snyder - Stanford University Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 HCFC1 (NB100-68209) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12CmycIggrabPk CH12 c-Myc immortalized c-Myc CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001944 1944 GSM912906 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12CmycIggrabPk None Peaks Immortal cells transcription factor; c-Myc-encoded proteins function in cell proliferation,differentiation and neoplastic disease B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 c-Myc TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12CjunIggrabPk CH12 c-Jun immortalized c-Jun CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001943 1943 GSM912901 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12CjunIggrabPk None Peaks Immortal cells Heterodimer of Fos and Jun constitute transcription factor AP1. Proto-oncogene c-Jun is a leucine-zipper. B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 c-Jun TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Znfmizdcp1ab65767IggrabPk CH12 ZNF-MIZD P immortalized ZNF-MIZD-CP1_(ab65767) CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003347 3347 GSM1003793 Snyder Stanford-m exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Znfmizdcp1ab65767IggrabPk None Peaks Immortal cells 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. B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 ZNF-MIZD-CP1 (ab65767) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Znf384hpa004051IggrabPk CH12 ZNF384 P immortalized ZNF384_(HPA004051) CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003348 3348 GSM1003796 Snyder Stanford-m exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Znf384hpa004051IggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 ZNF384 (HPA004051) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Zkscan1hpa006672IggrabPk CH12 ZKSCAN1_H immortalized ZKSCAN1_(HPA006672) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002787 2787 GSM1003782 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Zkscan1hpa006672IggrabPk None Peaks Immortal cells 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. B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 ZKSCAN1 (HPA006672) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Zc3h11anb10074650IggrabPk CH12 ZC3H11A P immortalized ZC3H11A_(NB100-74650) CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003346 3346 GSM1003792 Snyder Stanford-m exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Zc3h11anb10074650IggrabPk None Peaks Immortal cells 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. B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 ZC3H11A (NB100-74650) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Usf2IggmusPk CH12 USF2 immortalized USF2 CH12 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001957 1957 GSM912910 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Usf2IggmusPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 USF2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Ubfsc13125IggrabPk CH12 UBF_s immortalized UBF_(sc-13125) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-03-29 2012-12-29 wgEncodeEM002786 2786 GSM1003783 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Ubfsc13125IggrabPk None Peaks Immortal cells 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 B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 UBF (sc-13125) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12TbpIggmusPk CH12 TBP immortalized TBP CH12 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2011-07-19 2010-04-22 2011-01-22 wgEncodeEM001942 1942 GSM912900 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12TbpIggmusPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 TBP TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Smc3ab9263IggrabPk CH12 SMC3 immortalized SMC3_(ab9263) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEM001971 1971 GSM912930 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Smc3ab9263IggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 SMC3 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Sin3anb6001263IggrabPk CH12 SIN3A_N immortalized SIN3A_(NB600-1263) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-28 2012-11-28 wgEncodeEM002784 2784 GSM1003781 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Sin3anb6001263IggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 SIN3A (NB600-1263) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Rad21IggrabPk CH12 Rad21 immortalized Rad21 CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001956 1956 GSM912911 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Rad21IggrabPk None Peaks Immortal cells Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14 B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 Rad21 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Pol2s2IggrabPk CH12 Pol2S2 immortalized Pol2(phosphoS2) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-02-25 2011-11-25 wgEncodeEM001970 1970 GSM912931 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Pol2s2IggrabPk None Peaks Immortal cells RNA polymerase II, large subunit- specific for phosphorylated C-terminal domain. B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 Pol2(phoshoS2) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Pol2IggmusPk CH12 Pol2 immortalized Pol2 CH12 IgG-mus ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001941 1941 GSM912891 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Pol2IggmusPk None Peaks Immortal cells RNA Polymerase II B-cell lymphoma (GM12878 analog) Input signal from Normal Mouse IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 Pol2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12P300sc584IggrabPk CH12 p300 SC-584 immortalized p300_(SC-584) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001958 1958 GSM912920 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12P300sc584IggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 p300 (SC-584) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Nrf2IggrabPk CH12 Nrf2 P immortalized Nrf2 CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003337 3337 GSM1003800 Snyder Stanford-m exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Nrf2IggrabPk None Peaks Immortal cells Epitope corresponding to amino acids 1-180 mapping at the N-terminus of GABP-&#945 of human origin B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 Nrf2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12NelfeIggrabPk CH12 NELFe immortalized NELFe CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-20 2012-01-20 wgEncodeEM001977 1977 GSM912924 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12NelfeIggrabPk None Peaks Immortal cells NELF-E (RDBP) is a part of the negative elongation factor complex which binds to RNAPII to suppress elongation. B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 NELFe TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Mxi1af4185IggrabPk CH12 Mxi1 immortalized Mxi1_(AF4185) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-15 2011-12-14 wgEncodeEM001976 1976 GSM912925 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Mxi1af4185IggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 Mxi1 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Mazab85725IggrabPk CH12 MAZ P immortalized MAZ_(ab85725) CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003336 3336 GSM1003801 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Mazab85725IggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 MAZ (ab85725) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12MaxIggrabPk CH12 Max immortalized Max CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-07-08 2011-04-08 wgEncodeEM001955 1955 GSM912908 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12MaxIggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 Max TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Mafkab50322IggrabPk CH12 MafK_a immortalized MafK_(ab50322) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEM001980 1980 GSM912898 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Mafkab50322IggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 MafK (ab50322) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12JundIggrabPk CH12 JunD P immortalized JunD CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001940 1940 GSM912902 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12JundIggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 JunD TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Hcfc1nb10068209IggrabPk CH12 HCFC1 P immortalized HCFC1_(NB100-68209) CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-08-01 2013-05-01 wgEncodeEM003345 3345 GSM1003795 Snyder Stanford-m exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Hcfc1nb10068209IggrabPk None Peaks Immortal cells The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein). B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 HCFC1 (NB100-68209) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Gcn5IggrabPk CH12 GCN5 P immortalized GCN5 CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003335 3335 GSM1003802 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Gcn5IggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 GCN5 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Ets1IggrabPk CH12 ETS1 immortalized ETS1 CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-09-22 2012-06-21 wgEncodeEM002778 2778 GSM1003774 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Ets1IggrabPk None Peaks Immortal cells ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 ETS1 ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12E2f4IggrabPk CH12 E2F4 immortalized E2F4 CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2010-04-22 2011-01-22 wgEncodeEM001937 1937 GSM912912 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12E2f4IggrabPk None Peaks Immortal cells mapping at the C-terminus of E2F4 of human origin B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 E2F4 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12CtcfbIggrabPk CH12 CTCF immortalized CTCF_(SC-15914) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-06-29 2010-07-08 2011-04-08 wgEncodeEM001954 1954 GSM912909 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12CtcfbIggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 CTCF TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Corestsc30189IggrabPk CH12 COREST_s immortalized COREST_(sc-30189) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM002783 2783 GSM1003786 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Corestsc30189IggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 COREST (sc30189) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Chd2ab68301IggrabPk CH12 CHD2 immortalized CHD2_(AB68301) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-03-15 2011-12-14 wgEncodeEM001975 1975 GSM912926 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Chd2ab68301IggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 CHD2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Chd1nb10060411IggrabPk CH12 CHD1 P immortalized CHD1_(NB100-60411) CH12 IgG-rab ChipSeq ENCODE Jul 2012 Freeze 2012-06-29 2013-03-28 wgEncodeEM003334 3334 GSM1003803 Snyder Stanford-m exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Chd1nb10060411IggrabPk None Peaks Immortal cells 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 B-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 CHD1 (NB100-60411) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
wgEncodeSydhTfbsCh12Bhlhe40nb100IggrabPk CH12 BHLHE40 immortalized BHLHE40_(NB100-1800) CH12 IgG-rab ChipSeq ENCODE Mar 2012 Freeze 2011-04-28 2012-01-28 wgEncodeEM001979 1979 GSM912922 Snyder Stanford-m PeakSeq1.0 exp F B10.H-2aH-4bp/Wts wgEncodeSydhTfbsCh12Bhlhe40nb100IggrabPk None Peaks Immortal cells 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-cell lymphoma (GM12878 analog) Input signal from Normal Rabbit IgG ChIP-seq. Chromatin IP Sequencing Snyder Snyder - Stanford University Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 BHLHE40 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale Expression and Regulation 
transcriptome Transcriptome TROMER Transcriptome database Genes and Gene Predictions Description The transcriptome track shows gene predictions based on data from RefSeq and EMBL/GenBank. This is a moderately conservative set of predictions, requiring the support of either one GenBank full length RNA sequence, one RefSeq RNA, or one spliced EST. The track includes both protein-coding and non-coding transcripts. The CDS are predicted using ESTScan. Display Conventions and Configuration This track in general follows the display conventions for gene prediction tracks. The exons for putative noncoding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker. This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. Click here for more information about this feature. Further information on the predicted transcripts can be found on the Transcriptome Web interface. Methods The transcriptome is built using a multi-step pipeline: RefSeq and GenBank RNAs and ESTs are aligned to the genome with SIBsim4, keeping only the best alignments for each RNA. Alignments are broken up at non-intronic gaps, with small isolated fragments thrown out. A splicing graph is created for each set of overlapping alignments. This graph has an edge for each exon or intron, and a vertex for each splice site, start, and end. Each RNA that contributes to an edge is kept as evidence for that edge. The graph is traversed to generate all unique transcripts. The traversal is guided by the initial RNAs to avoid a combinatorial explosion in alternative splicing. Protein predictions are generated. Credits The transcriptome track was produced on the Vital-IT high-performance computing platform using a computational pipeline developed by Christian Iseli with help from colleagues at the Ludwig institute for Cancer Research and the Swiss Institute of Bioinformatics. It is based on data from NCBI RefSeq and GenBank/ EMBL. Our thanks to the people running these databases and to the scientists worldwide who have made contributions to them. References Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779 
tRNAs tRNA Genes Transfer RNA Genes Identified with tRNAscan-SE Genes and Gene Predictions Description This track displays tRNA genes predicted by using tRNAscan-SE v.1.23. tRNAscan-SE is an integrated program that uses tRNAscan (Fichant) and an A/B box motif detection algorithm (Pavesi) as pre-filters to obtain an initial list of tRNA candidates. The program then filters these candidates with a covariance model-based search program COVE (Eddy) to obtain a highly specific set of primary sequence and secondary structure predictions that represent 99-100% of true tRNAs with a false positive rate of fewer than 1 per 15 gigabases. Detailed tRNA annotations for eukaryotes, bacteria, and archaea are available at Genomic tRNA Database (GtRNAdb). What does the tRNAscan-SE score mean? Anything with a score above 20 bits is likely to be derived from a tRNA, although this does not indicate whether the tRNA gene still encodes a functional tRNA molecule (i.e. tRNA-derived SINES probably do not function in the ribosome in translation). Vertebrate tRNAs with scores of &gt;60.0 (bits) are likely to encode functional tRNA genes, and those with scores below ~45 have sequence or structural features that indicate they probably are no longer involved in translation. tRNAs with scores between 45-60 bits are in the &quot;grey&quot; zone, and may or may not have all the required features to be functional. In these cases, tRNAs should be inspected carefully for loss of specific primary or secondary structure features (usually in alignments with other genes of the same isotype), in order to make a better educated guess. These rough score range guides are not exact, nor are they based on specific biochemical studies of atypical tRNA features, so please treat them accordingly. Please note that tRNA genes marked as &quot;Pseudo&quot; are low scoring predictions that are mostly pseudogenes or tRNA-derived elements. These genes do not usually fold into a typical cloverleaf tRNA secondary structure and the provided images of the predicted secondary structures may appear rotated. Credits Both tRNAscan-SE and GtRNAdb are maintained by the Lowe Lab at UCSC. Cove-predicted tRNA secondary structures were rendered by NAVIEW (c) 1988 Robert E. Bruccoleri. References When making use of these data, please cite the following articles: Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009 Jan;37(Database issue):D93-7. PMID: 18984615; PMC: PMC2686519 Eddy SR, Durbin R. RNA sequence analysis using covariance models. Nucleic Acids Res. 1994 Jun 11;22(11):2079-88. PMID: 8029015; PMC: PMC308124 Fichant GA, Burks C. Identifying potential tRNA genes in genomic DNA sequences. J Mol Biol. 1991 Aug 5;220(3):659-71. PMID: 1870126 Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997 Mar 1;25(5):955-64. PMID: 9023104; PMC: PMC146525 Pavesi A, Conterio F, Bolchi A, Dieci G, Ottonello S. Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions. Nucleic Acids Res. 1994 Apr 11;22(7):1247-56. PMID: 8165140; PMC: PMC523650 
targetScanS TS miRNA sites TargetScan miRNA Regulatory Sites Expression and Regulation Description This track shows conserved mammalian microRNA regulatory target sites for conserved microRNA families in the 3' UTR regions of Refseq Genes, as predicted by TargetScanMouse 5.1. Method Putative miRNA binding sites in UTRs were identified using seven-nucleotide seed regions from all known miRNA families conserved across mammals. Using all mouse RefSeq transcripts and CDS annotation from NCBI, aligned vertebrate 3' UTRs were extracted from multiz alignments and masked for overlap with protein-coding sequences. These 3' UTRs were scanned to identify conserved matches to the miRNA seed region, as in Friedman et al. (2009). These sites were then assigned a percentile rank (0 to 100) based on their context score (Grimson et al., 2007). For further details of the methods used to generate this annotation, see the references and the TargetScan website. Credit Thanks to George Bell of Bioinformatics and Research Computing at the Whitehead Institute for providing this annotation, which was generated in collaboration with the labs of David Bartel and Chris Burge. Additional information on microRNA target prediction is available on the TargetScan website. References Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009 Jan;19(1):92-105. PMID: 18955434; PMC: PMC2612969 Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007 Jul 6;27(1):91-105. PMID: 17612493; PMC: PMC3800283 Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005 Jan 14;120(1):15-20. PMID: 15652477 
knownAlt UCSC Alt Events Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes Genes and Gene Predictions Description This track shows various types of alternative splicing and other events that result in more than a single transcript from the same gene. The label by an item describes the type of event. The events are: Alternate Promoter (altPromoter) - Transcription starts at multiple places. The altPromoter extends from 100 bases before to 50 bases after transcription start. Alternate Finish Site (altFinish) - Transcription ends at multiple places. Cassette Exon (cassetteExon) - Exon is present in some transcripts but not others. These are found by looking for exons that overlap an intron in the same transcript. Retained Intron (retainedIntron) - Introns are spliced out in some transcripts but not others. In some cases, particularly when the intron is near the 3' end, this can reflect an incompletely processed transcript rather than a true alt-splicing event. Overlapping Exon (bleedingExon) - Initial or terminal exons overlap in an intron in another transcript. These often are associated with incompletely processed transcripts. Alternate 3' End (altThreePrime) - Variations on the 3' end of an intron. Alternate 5' End (altFivePrime) - Variations on the 5' end of an intron. Intron Ends have AT/AC (atacIntron) - An intron with AT/AC ends rather than the usual GT/AG. These are associated with the minor spliceosome. Strange Intron Ends (strangeSplice) - An intron with ends that are not GT/AG, GC/AG, or AT/AC. These are usually artifacts of some sort due to sequencing error or polymorphism. Credits This track is based on an analysis by the txgAnalyse program of splicing graphs produced by the txGraph program. Both of these programs were written by Jim Kent at UCSC. 
wgEncodeUwDgf UW DNaseI DGF GSE40869 DNaseI Digital Genomic Footprinting from ENCODE/University of Washington Expression and Regulation Description This track, produced as part of the mouse ENCODE Project, contains deep sequencing DNase data that will be used to identify sites where regulatory factors bind to the genome (footprints). Footprinting is a technique used to define the DNA sequences that interact with and bind DNA-binding proteins, such as transcription factors, zinc-finger proteins, hormone-receptor complexes, and other chromatin-modulating factors like CTCF. The technique depends upon the strength and tight nature of protein-DNA interactions. In their native chromatin state, DNA sequences that interact directly with DNA-binding proteins are relatively protected from DNA degrading endonucleases, while the exposed/unbound portions are readily degraded by such endonucleases. A massively parallel next-generation sequencing technique to define the DNase hypersensitive sites in the genome was adopted. The DNase samples were sequenced using next-generation sequencing machines to significantly higher depths of 300-fold or greater. This produces a base-pair level resolution of the DNase susceptibility maps of the native chromatin state. These base-pair resolution maps represent and are dependent upon the nature and the specificity of interaction of the DNA with the regulatory/modulatory proteins binding at specific loci in the genome; thus they represent the native chromatin state of the genome under investigation. The deep sequencing approach has been used to define the footprint landscape of the genome by identifying DNA motifs that interact with known or novel DNA binding proteins. 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 DNaseI hypersensitive zones identified using the HotSpot algorithm. Peaks DNaseI hypersensitive sites (DHSs) identified as signal peaks within FDR 1.0% hypersensitive zones. Signal Per-base count of sequence reads whose 5' end (corresponding to a DNaseI-induced DNA cut) coincides with the given position. Raw Signal The density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). NOTE: The names of the signal views in this track are reversed from conventions used in other ENCODE tracks, where the less processed signal is termed "Raw". DNaseI sensitivity is shown as the absolute density of in vivo cleavage sites across the genome mapped using the Digital DNaseI methodology (see below). 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. Digital DNaseI was performed by DNaseI digestion of intact nuclei, followed by isolating DNaseI "double-hit" fragments (Sabo et al., 2006), and direct sequencing of fragment ends (which correspond to in vivo DNaseI cleavage sites) using the Solexa platform (27 bp reads). High-quality reads were mapped to the NCBI37/mm9 mouse genome using Bowtie 0.12.5; only unique mappings were kept. DNaseI sensitivity is directly reflected in 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). DNaseI hypersensitive zones (HotSpots) were identified using the HotSpot algorithm (Sabo et al., 2004). False discovery rate thresholds of 1.0% (FDR 0.01) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36-mers. DNaseI hypersensitive sites (DHSs or Peaks) were identified as signal peaks within 1.0% (FDR 0.01) hypersensitive zones using a peak-finding algorithm. Only DNase Solexa libraries from unique cell types producing the highest quality data, as defined by Percent Tags in Hotspots (PTIH ~40%), were designated for deep sequencing to a depth of over 200 million tags. Verification Results were validated by conventional DNaseI hypersensitivity assays using end-labeling/Southern blotting methods. Release Notes This is Release 1 (Aug 2012) of this track, which contains a total of 22 DNaseI Digital Genomic Footprinting (DNaseI DGF) 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. Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods. 2006 Jul;3(7):511-8. 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. 
wgEncodeUwDgfViewSignal Signal DNaseI Digital Genomic Footprinting from ENCODE/University of Washington Expression and Regulation 
wgEncodeUwDgfZhbtc4129olaME0SigRep1 ZhBTc4 E0 S E0 ZhBTc4 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002920 2920 GSM1003822 Stam UW-m DS17616 None 1 Illumina_HiSeq_2000 M 129/Ola wgEncodeUwDgfZhbtc4129olaME0SigRep1 None Signal Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ZhBTc4 E0 129/Ola DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfZhbtc4129olaME0Diffb24hSigRep1 ZhBTc4 diff E0 S E0 ZhBTc4 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002921 2921 GSM1003821 Stam UW-m DS17562 None 1 Illumina_HiSeq_2000 M 129/Ola wgEncodeUwDgfZhbtc4129olaME0Diffb24hSigRep1 None diffProtB_24hr Signal Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 24 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam) Signal ZhBTc4 E0 129/Ola differentiated 24 hr DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfWbrainC57bl6ME14halfSigRep1 Brain E14.5 S E14.5 WholeBrain DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002913 2913 GSM1003828 Stam UW-m DS14536 None 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfWbrainC57bl6ME14halfSigRep1 Pooled Signal Embryonic day 14.5 Whole Brain DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Brain E14.5 C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfWbrainC57bl6MAdult8wksSigRep1 Brain 8w S adult-8wks WholeBrain DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002909 2909 GSM1003823 Stam UW-m DS12727 None 1 Illumina_GA2x M C57BL/6 wgEncodeUwDgfWbrainC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Whole Brain DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina Genome Analyzer IIx Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Brain 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTregaC57bl6MAdult8wksSigRep1 TReg-Act 8w S adult-8wks TReg-Activated DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002919 2919 GSM1003834 Stam UW-m DS20149 None 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTregaC57bl6MAdult8wksSigRep1 None Signal Adult 8 weeks Activated primary T regulatory cells, isolated ex vivo DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal TReg-Activated 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTregC57bl6MAdult8wksSigRep1 TReg 8w S adult-8wks TReg DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002911 2911 GSM1003826 Stam UW-m DS17864 None 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTregC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Regulatory T cells CD4+,CD25+ DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal TReg 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTnaiveC57bl6MAdult8wksSigRep2 T-Naive 8w S 2 adult-8wks T-Naive DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002910 2910 GSM1003825 Stam UW-m DS16171 None 2 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTnaiveC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Naive T cells: CD4+, CD25- DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal T-Naive 8w C57BL/6 DNaseI DGF Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTnaiveC57bl6MAdult8wksSigRep1 T-Naive 8w S 1 adult-8wks T-Naive DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002910 2910 GSM1003825 Stam UW-m DS17080 None 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTnaiveC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Naive T cells: CD4+, CD25- DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal T-Naive 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfThymusC57bl6MAdult8wksSigRep1 Thymus 8w S adult-8wks Thymus DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002912 2912 GSM1003827 Stam UW-m DS18819 None 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfThymusC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Thymus DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Thymus 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfThelpaC57bl6MAdult8wksSigRep1 THelp-Act 8w S adult-8wks THelper-Activated DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002918 2918 GSM1003833 Stam UW-m DS17070 None 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfThelpaC57bl6MAdult8wksSigRep1 None Signal Adult 8 weeks Activated primary CD4 effector cells, isolated ex vivo DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Signal THelper-Activated 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfRetinaC57bl6MNew1daysSigRep1 Retina 1day S newborn-1days Retina DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002917 2917 GSM1003832 Stam UW-m DS20004 None 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfRetinaC57bl6MNew1daysSigRep1 Pooled Signal Newborn 1 day Retina DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Retina Newborn 1 Day C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfNih3t3NihsMImmortalSigRep1 NIH-3T3 Immt S immortalized NIH-3T3 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002916 2916 GSM1003831 Stam UW-m DS16900 None 1 Illumina_HiSeq_2000 M NIH/Swiss wgEncodeUwDgfNih3t3NihsMImmortalSigRep1 None Signal Immortal cells fibroblast DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Signal NIH-3T3 Immortal NIH/Swiss DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfMelUknImmortalSigRep1 MEL Immt S immortalized MEL DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002908 2908 GSM1003824 Stam UW-m DS13036 None 1 Illumina_HiSeq_2000 M Unknown wgEncodeUwDgfMelUknImmortalSigRep1 Pooled Signal Immortal cells Leukemia (K562 analog) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male Unknown strain origin Tissue obtained from pooling samples from various sample organisms Signal MEL Immortal DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfLungC57bl6MAdult8wksSigRep1 Lung 8w S adult-8wks Lung DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002907 2907 GSM1003817 Stam UW-m DS14479 None 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfLungC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Lung DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Lung 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfLiverC57bl6MAdult8wksSigRep1 Liver 8w S adult-8wks Liver DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002906 2906 GSM1003818 Stam UW-m DS14605 None 1 Illumina_GA2x M C57BL/6 wgEncodeUwDgfLiverC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Liver DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina Genome Analyzer IIx Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Liver 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfKidneyC57bl6MAdult8wksSigRep1 Kidney 8w S adult-8wks Kidney DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002905 2905 GSM1003819 Stam UW-m DS13948 None 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfKidneyC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Kidney DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Kidney 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfHeartC57bl6MAdult8wksSigRep1 Heart 8w S adult-8wks Heart DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002904 2904 GSM1003820 Stam UW-m DS18138 None 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfHeartC57bl6MAdult8wksSigRep1 Individual Signal Adult 8 weeks Heart DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Heart 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfEscj7129s1ME0SigRep1 ES-CJ7 E0 S E0 ES-CJ7 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002915 2915 GSM1003830 Stam UW-m DS13320 None 1 Illumina_HiSeq_2000 M 129S1/SVImJ wgEncodeUwDgfEscj7129s1ME0SigRep1 None Signal Embryonic day 0 (stem cell) ES-cells were originally isolated from 129S1/SVImJ mice by Swiatek PJ et al. in 1993 ("Perinatal lethality and defects in hindbrain development in mice homozygous for a targeted mutation of the zinc finger gene Krox20". Swiatek PJ, Gridley T. Genes Dev. 1993 Nov,7(11):2071-84.) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male Control inbred strain of the steel-derived ES cells. Signal ES-CJ7 E0 129S1/SVImJ DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksSigRep1 Bcell CD43- 8w S adult-8wks B-cell_(CD43-) DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002903 2903 GSM1003813 Stam UW-m DS17866 None 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks mouse spleen B cells, CD43-,CD11b- DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal B-cell (CD43-) 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksSigRep1 Bcell CD19+ 8w S adult-8wks B-cell_(CD19+) DnaseDgf ENCODE Mar 2012 Freeze 2012-01-18 2011-12-17 2012-09-17 wgEncodeEM002902 2902 GSM1003814 Stam UW-m DS16168 None 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks B Cell , CD19+ DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal B-cell (CD19+) 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfA20BalbcannMImmortalSigRep1 A20 Immt S immortalized A20 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002914 2914 GSM1003829 Stam UW-m DS16695 None 1 Illumina_HiSeq_2000 M BALB/cAnN wgEncodeUwDgfA20BalbcannMImmortalSigRep1 None Signal Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male ccMyeloma high incidence H2d Signal A20 Immortal BALB/cAnN DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgf416bB6d2f1jImmortalSigRep1 416B Immt S immortalized 416B DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002901 2901 GSM1003815 Stam UW-m DS14099 None 1 Illumina_HiSeq_2000 M B6D2F1/J wgEncodeUwDgf416bB6d2f1jImmortalSigRep1 Pooled Signal Immortal cells myeloid progenitor cells, CD34+ DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Tissue obtained from pooling samples from various sample organisms Signal 416B Immortal B6D2F1/J DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgf3134RiiiMImmortalSigRep1 3134 Immt S immortalized 3134 DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002900 2900 GSM1003816 Stam UW-m DS8497 None 1 Illumina_GA2x M RIII wgEncodeUwDgf3134RiiiMImmortalSigRep1 None Signal Immortal cells Mammary DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina Genome Analyzer IIx Male High mammary tumor incidence in unfostered substrains. Signal 3134 Immortal RIII DNaseI DGF Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfViewRawSignal RawSignal DNaseI Digital Genomic Footprinting from ENCODE/University of Washington Expression and Regulation 
wgEncodeUwDgfZhbtc4129olaME0RawRep1 ZhBTc4 E0 R E0 ZhBTc4 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002920 2920 GSM1003822 Stam UW-m DS17616 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M 129/Ola wgEncodeUwDgfZhbtc4129olaME0RawRep1 None RawSignal Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Shows the density of mapped reads on the plus and minus strands (wiggle format) ZhBTc4 E0 129/Ola DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfZhbtc4129olaME0Diffb24hRawRep1 ZhBTc4 diff E0 R E0 ZhBTc4 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002921 2921 GSM1003821 Stam UW-m DS17562 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M 129/Ola wgEncodeUwDgfZhbtc4129olaME0Diffb24hRawRep1 None diffProtB_24hr RawSignal Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 24 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam) Shows the density of mapped reads on the plus and minus strands (wiggle format) ZhBTc4 E0 129/Ola differentiated 24 hr DNaseI DGF Raw Signal Rep 1 ENCODE/UW Expression and Regulation 
wgEncodeUwDgfWbrainC57bl6ME14halfRawRep1 Brain E14.5 R E14.5 WholeBrain DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002913 2913 GSM1003828 Stam UW-m DS14536 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfWbrainC57bl6ME14halfRawRep1 Pooled RawSignal Embryonic day 14.5 Whole Brain DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) Brain E14.5 C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfWbrainC57bl6MAdult8wksRawRep1 Brain 8w R adult-8wks WholeBrain DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002909 2909 GSM1003823 Stam UW-m DS12727 WindowDensity-bin20-win+/-75 1 Illumina_GA2x M C57BL/6 wgEncodeUwDgfWbrainC57bl6MAdult8wksRawRep1 Pooled RawSignal Adult 8 weeks Whole Brain DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina Genome Analyzer IIx Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) Brain 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTregaC57bl6MAdult8wksRawRep1 TReg-Act 8w R adult-8wks TReg-Activated DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002919 2919 GSM1003834 Stam UW-m DS20149 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTregaC57bl6MAdult8wksRawRep1 None RawSignal Adult 8 weeks Activated primary T regulatory cells, isolated ex vivo DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Shows the density of mapped reads on the plus and minus strands (wiggle format) TReg-Activated 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTregC57bl6MAdult8wksRawRep1 TReg 8w R adult-8wks TReg DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002911 2911 GSM1003826 Stam UW-m DS17864 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTregC57bl6MAdult8wksRawRep1 Pooled RawSignal Adult 8 weeks Regulatory T cells CD4+,CD25+ DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) TReg 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTnaiveC57bl6MAdult8wksRawRep2 T-Naive 8w R 2 adult-8wks T-Naive DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002910 2910 GSM1003825 Stam UW-m DS16171 WindowDensity-bin20-win+/-75 2 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTnaiveC57bl6MAdult8wksRawRep2 Pooled RawSignal Adult 8 weeks Naive T cells: CD4+, CD25- DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) T-Naive 8w C57BL/6 DNaseI DGF Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTnaiveC57bl6MAdult8wksRawRep1 T-Naive 8w R 1 adult-8wks T-Naive DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002910 2910 GSM1003825 Stam UW-m DS17080 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTnaiveC57bl6MAdult8wksRawRep1 Pooled RawSignal Adult 8 weeks Naive T cells: CD4+, CD25- DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) T-Naive 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfThymusC57bl6MAdult8wksRawRep1 Thymus 8w R adult-8wks Thymus DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002912 2912 GSM1003827 Stam UW-m DS18819 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfThymusC57bl6MAdult8wksRawRep1 Pooled RawSignal Adult 8 weeks Thymus DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) Thymus 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfThelpaC57bl6MAdult8wksRawRep1 THelp-Act 8w R adult-8wks THelper-Activated DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002918 2918 GSM1003833 Stam UW-m DS17070 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfThelpaC57bl6MAdult8wksRawRep1 None RawSignal Adult 8 weeks Activated primary CD4 effector cells, isolated ex vivo DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Shows the density of mapped reads on the plus and minus strands (wiggle format) THelper-Activated 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfRetinaC57bl6MNew1daysRawRep1 Retina 1day R newborn-1days Retina DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002917 2917 GSM1003832 Stam UW-m DS20004 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfRetinaC57bl6MNew1daysRawRep1 Pooled RawSignal Newborn 1 day Retina DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) Retina Newborn 1 Day C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfNih3t3NihsMImmortalRawRep1 NIH-3T3 Immt R immortalized NIH-3T3 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002916 2916 GSM1003831 Stam UW-m DS16900 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M NIH/Swiss wgEncodeUwDgfNih3t3NihsMImmortalRawRep1 None RawSignal Immortal cells fibroblast DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Shows the density of mapped reads on the plus and minus strands (wiggle format) NIH-3T3 Immortal NIH/Swiss DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfMelUknImmortalRawRep1 MEL Immt R immortalized MEL DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002908 2908 GSM1003824 Stam UW-m DS13036 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M Unknown wgEncodeUwDgfMelUknImmortalRawRep1 Pooled RawSignal Immortal cells Leukemia (K562 analog) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male Unknown strain origin Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) MEL Immortal DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfLungC57bl6MAdult8wksRawRep1 Lung 8w R adult-8wks Lung DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002907 2907 GSM1003817 Stam UW-m DS14479 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfLungC57bl6MAdult8wksRawRep1 Pooled RawSignal Adult 8 weeks Lung DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) Lung 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfLiverC57bl6MAdult8wksRawRep1 Liver 8w R adult-8wks Liver DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002906 2906 GSM1003818 Stam UW-m DS14605 WindowDensity-bin20-win+/-75 1 Illumina_GA2x M C57BL/6 wgEncodeUwDgfLiverC57bl6MAdult8wksRawRep1 Pooled RawSignal Adult 8 weeks Liver DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina Genome Analyzer IIx Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) Liver 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfKidneyC57bl6MAdult8wksRawRep1 Kidney 8w R adult-8wks Kidney DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002905 2905 GSM1003819 Stam UW-m DS13948 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfKidneyC57bl6MAdult8wksRawRep1 Pooled RawSignal Adult 8 weeks Kidney DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) Kidney 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfHeartC57bl6MAdult8wksRawRep1 Heart 8w R adult-8wks Heart DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002904 2904 GSM1003820 Stam UW-m DS18138 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfHeartC57bl6MAdult8wksRawRep1 Individual RawSignal Adult 8 weeks Heart DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows the density of mapped reads on the plus and minus strands (wiggle format) Heart 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfEscj7129s1ME0RawRep1 ES-CJ7 E0 R E0 ES-CJ7 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002915 2915 GSM1003830 Stam UW-m DS13320 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M 129S1/SVImJ wgEncodeUwDgfEscj7129s1ME0RawRep1 None RawSignal Embryonic day 0 (stem cell) ES-cells were originally isolated from 129S1/SVImJ mice by Swiatek PJ et al. in 1993 ("Perinatal lethality and defects in hindbrain development in mice homozygous for a targeted mutation of the zinc finger gene Krox20". Swiatek PJ, Gridley T. Genes Dev. 1993 Nov,7(11):2071-84.) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male Control inbred strain of the steel-derived ES cells. Shows the density of mapped reads on the plus and minus strands (wiggle format) ES-CJ7 E0 129S1/SVImJ DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksRawRep1 Bcell CD43- 8w R adult-8wks B-cell_(CD43-) DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002903 2903 GSM1003813 Stam UW-m DS17866 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksRawRep1 Pooled RawSignal Adult 8 weeks mouse spleen B cells, CD43-,CD11b- DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) B-cell (CD43-) 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksRawRep1 Bcell CD19+ 8w R adult-8wks B-cell_(CD19+) DnaseDgf ENCODE Mar 2012 Freeze 2012-01-18 2011-12-17 2012-09-17 wgEncodeEM002902 2902 GSM1003814 Stam UW-m DS16168 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksRawRep1 Pooled RawSignal Adult 8 weeks B Cell , CD19+ DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) B-cell (CD19+) 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfA20BalbcannMImmortalRawRep1 A20 Immt R immortalized A20 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002914 2914 GSM1003829 Stam UW-m DS16695 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M BALB/cAnN wgEncodeUwDgfA20BalbcannMImmortalRawRep1 None RawSignal Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male ccMyeloma high incidence H2d Shows the density of mapped reads on the plus and minus strands (wiggle format) A20 Immortal BALB/cAnN DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgf416bB6d2f1jImmortalRawRep1 416B Immt R immortalized 416B DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002901 2901 GSM1003815 Stam UW-m DS14099 WindowDensity-bin20-win+/-75 1 Illumina_HiSeq_2000 M B6D2F1/J wgEncodeUwDgf416bB6d2f1jImmortalRawRep1 Pooled RawSignal Immortal cells myeloid progenitor cells, CD34+ DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Tissue obtained from pooling samples from various sample organisms Shows the density of mapped reads on the plus and minus strands (wiggle format) 416B Immortal B6D2F1/J DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgf3134RiiiMImmortalRawRep1 3134 Immt R immortalized 3134 DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002900 2900 GSM1003816 Stam UW-m DS8497 WindowDensity-bin20-win+/-75 1 Illumina_GA2x M RIII wgEncodeUwDgf3134RiiiMImmortalRawRep1 None RawSignal Immortal cells Mammary DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina Genome Analyzer IIx Male High mammary tumor incidence in unfostered substrains. Shows the density of mapped reads on the plus and minus strands (wiggle format) 3134 Immortal RIII DNaseI DGF Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfViewPeaks Peaks DNaseI Digital Genomic Footprinting from ENCODE/University of Washington Expression and Regulation 
wgEncodeUwDgfZhbtc4129olaME0PkRep1 ZhBTc4 E0 P E0 ZhBTc4 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002920 2920 GSM1003822 Stam UW-m DS17616 lmax-v1.1 1 Illumina_HiSeq_2000 M 129/Ola wgEncodeUwDgfZhbtc4129olaME0PkRep1 None Peaks Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ZhBTc4 E0 129/Ola DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfZhbtc4129olaME0Diffb24hPkRep1 ZhBTc4 diff E0 P E0 ZhBTc4 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002921 2921 GSM1003821 Stam UW-m DS17562 lmax-v1.1 1 Illumina_HiSeq_2000 M 129/Ola wgEncodeUwDgfZhbtc4129olaME0Diffb24hPkRep1 None diffProtB_24hr Peaks Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 24 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam) Regions of enriched signal in experiment ZhBTc4 E0 129/Ola differentiated 24 hr DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfWbrainC57bl6ME14halfPkRep1 Brain E14.5 P E14.5 WholeBrain DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002913 2913 GSM1003828 Stam UW-m DS14536 lmax-v1.1 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfWbrainC57bl6ME14halfPkRep1 Pooled Peaks Embryonic day 14.5 Whole Brain DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Brain E14.5 C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfWbrainC57bl6MAdult8wksPkRep1 Brain 8w P adult-8wks WholeBrain DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002909 2909 GSM1003823 Stam UW-m DS12727 lmax-v1.1 1 Illumina_GA2x M C57BL/6 wgEncodeUwDgfWbrainC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Whole Brain DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina Genome Analyzer IIx Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Brain 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTregaC57bl6MAdult8wksPkRep1 TReg-Act 8w P adult-8wks TReg-Activated DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002919 2919 GSM1003834 Stam UW-m DS20149 lmax-v1.1 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTregaC57bl6MAdult8wksPkRep1 None Peaks Adult 8 weeks Activated primary T regulatory cells, isolated ex vivo DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment TReg-Activated 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTregC57bl6MAdult8wksPkRep1 TReg 8w P adult-8wks TReg DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002911 2911 GSM1003826 Stam UW-m DS17864 lmax-v1.1 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTregC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Regulatory T cells CD4+,CD25+ DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment TReg 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTnaiveC57bl6MAdult8wksPkRep2 T-Naive 8w P 2 adult-8wks T-Naive DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002910 2910 GSM1003825 Stam UW-m DS16171 lmax-v1.1 2 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTnaiveC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Naive T cells: CD4+, CD25- DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment T-Naive 8w C57BL/6 DNaseI DGF Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTnaiveC57bl6MAdult8wksPkRep1 T-Naive 8w P 1 adult-8wks T-Naive DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002910 2910 GSM1003825 Stam UW-m DS17080 lmax-v1.1 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTnaiveC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Naive T cells: CD4+, CD25- DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment T-Naive 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfThymusC57bl6MAdult8wksPkRep1 Thymus 8w P adult-8wks Thymus DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002912 2912 GSM1003827 Stam UW-m DS18819 lmax-v1.1 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfThymusC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Thymus DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Thymus 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfThelpaC57bl6MAdult8wksPkRep1 THelp-Act 8w P adult-8wks THelper-Activated DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002918 2918 GSM1003833 Stam UW-m DS17070 lmax-v1.1 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfThelpaC57bl6MAdult8wksPkRep1 None Peaks Adult 8 weeks Activated primary CD4 effector cells, isolated ex vivo DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment THelper-Activated 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfRetinaC57bl6MNew1daysPkRep1 Retina 1day P newborn-1days Retina DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002917 2917 GSM1003832 Stam UW-m DS20004 lmax-v1.1 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfRetinaC57bl6MNew1daysPkRep1 Pooled Peaks Newborn 1 day Retina DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Retina Newborn 1 Day C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfNih3t3NihsMImmortalPkRep1 NIH-3T3 Immt P immortalized NIH-3T3 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002916 2916 GSM1003831 Stam UW-m DS16900 lmax-v1.1 1 Illumina_HiSeq_2000 M NIH/Swiss wgEncodeUwDgfNih3t3NihsMImmortalPkRep1 None Peaks Immortal cells fibroblast DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Regions of enriched signal in experiment NIH-3T3 Immortal NIH/Swiss DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfMelUknImmortalPkRep1 MEL Immt P immortalized MEL DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002908 2908 GSM1003824 Stam UW-m DS13036 lmax-v1.1 1 Illumina_HiSeq_2000 M Unknown wgEncodeUwDgfMelUknImmortalPkRep1 Pooled Peaks Immortal cells Leukemia (K562 analog) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male Unknown strain origin Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment MEL Immortal DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfLungC57bl6MAdult8wksPkRep1 Lung 8w P adult-8wks Lung DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002907 2907 GSM1003817 Stam UW-m DS14479 lmax-v1.1 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfLungC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Lung DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Lung 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfLiverC57bl6MAdult8wksPkRep1 Liver 8w P adult-8wks Liver DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002906 2906 GSM1003818 Stam UW-m DS14605 lmax-v1.1 1 Illumina_GA2x M C57BL/6 wgEncodeUwDgfLiverC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Liver DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina Genome Analyzer IIx Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Liver 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfKidneyC57bl6MAdult8wksPkRep1 Kidney 8w P adult-8wks Kidney DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002905 2905 GSM1003819 Stam UW-m DS13948 lmax-v1.1 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfKidneyC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Kidney DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Kidney 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfHeartC57bl6MAdult8wksPkRep1 Heart 8w P adult-8wks Heart DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002904 2904 GSM1003820 Stam UW-m DS18138 lmax-v1.1 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfHeartC57bl6MAdult8wksPkRep1 Individual Peaks Adult 8 weeks Heart DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Heart 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfEscj7129s1ME0PkRep1 ES-CJ7 E0 P E0 ES-CJ7 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002915 2915 GSM1003830 Stam UW-m DS13320 lmax-v1.1 1 Illumina_HiSeq_2000 M 129S1/SVImJ wgEncodeUwDgfEscj7129s1ME0PkRep1 None Peaks Embryonic day 0 (stem cell) ES-cells were originally isolated from 129S1/SVImJ mice by Swiatek PJ et al. in 1993 ("Perinatal lethality and defects in hindbrain development in mice homozygous for a targeted mutation of the zinc finger gene Krox20". Swiatek PJ, Gridley T. Genes Dev. 1993 Nov,7(11):2071-84.) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male Control inbred strain of the steel-derived ES cells. Regions of enriched signal in experiment ES-CJ7 E0 129S1/SVImJ DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksPkRep1 Bcell CD43- 8w P adult-8wks B-cell_(CD43-) DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002903 2903 GSM1003813 Stam UW-m DS17866 lmax-v1.1 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks mouse spleen B cells, CD43-,CD11b- DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment B-cell (CD43-) 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksPkRep1 Bcell CD19+ 8w P adult-8wks B-cell_(CD19+) DnaseDgf ENCODE Mar 2012 Freeze 2012-01-18 2011-12-17 2012-09-17 wgEncodeEM002902 2902 GSM1003814 Stam UW-m DS16168 lmax-v1.1 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks B Cell , CD19+ DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment B-cell (CD19+) 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfA20BalbcannMImmortalPkRep1 A20 Immt P immortalized A20 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002914 2914 GSM1003829 Stam UW-m DS16695 lmax-v1.1 1 Illumina_HiSeq_2000 M BALB/cAnN wgEncodeUwDgfA20BalbcannMImmortalPkRep1 None Peaks Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male ccMyeloma high incidence H2d Regions of enriched signal in experiment A20 Immortal BALB/cAnN DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgf416bB6d2f1jImmortalPkRep1 416B Immt P immortalized 416B DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002901 2901 GSM1003815 Stam UW-m DS14099 lmax-v1.1 1 Illumina_HiSeq_2000 M B6D2F1/J wgEncodeUwDgf416bB6d2f1jImmortalPkRep1 Pooled Peaks Immortal cells myeloid progenitor cells, CD34+ DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment 416B Immortal B6D2F1/J DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgf3134RiiiMImmortalPkRep1 3134 Immt P immortalized 3134 DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002900 2900 GSM1003816 Stam UW-m DS8497 lmax-v1.1 1 Illumina_GA2x M RIII wgEncodeUwDgf3134RiiiMImmortalPkRep1 None Peaks Immortal cells Mammary DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina Genome Analyzer IIx Male High mammary tumor incidence in unfostered substrains. Regions of enriched signal in experiment 3134 Immortal RIII DNaseI DGF Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfViewHotspots Hotspots DNaseI Digital Genomic Footprinting from ENCODE/University of Washington Expression and Regulation 
wgEncodeUwDgfZhbtc4129olaME0HotspotsRep1 ZhBTc4 E0 H E0 ZhBTc4 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002920 2920 GSM1003822 Stam UW-m DS17616 Hotspot-v5.2 1 Illumina_HiSeq_2000 M 129/Ola wgEncodeUwDgfZhbtc4129olaME0HotspotsRep1 None Hotspots Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. ChIP-seq affinity zones identified using the HotSpot algorithm ZhBTc4 E0 129/Ola DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfZhbtc4129olaME0Diffb24hHotspotsRep1 ZhBTc4 diff E0 H E0 ZhBTc4 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002921 2921 GSM1003821 Stam UW-m DS17562 Hotspot-v5.2 1 Illumina_HiSeq_2000 M 129/Ola wgEncodeUwDgfZhbtc4129olaME0Diffb24hHotspotsRep1 None diffProtB_24hr Hotspots Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 24 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm ZhBTc4 E0 129/Ola differentiated 24 hr DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfWbrainC57bl6ME14halfHotspotsRep1 Brain E14.5 H E14.5 WholeBrain DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002913 2913 GSM1003828 Stam UW-m DS14536 Hotspot-v5.2 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfWbrainC57bl6ME14halfHotspotsRep1 Pooled Hotspots Embryonic day 14.5 Whole Brain DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Brain E14.5 C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfWbrainC57bl6MAdult8wksHotspotsRep1 Brain 8w H adult-8wks WholeBrain DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002909 2909 GSM1003823 Stam UW-m DS12727 Hotspot-v5.2 1 Illumina_GA2x M C57BL/6 wgEncodeUwDgfWbrainC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Whole Brain DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina Genome Analyzer IIx Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Brain 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTregaC57bl6MAdult8wksHotspotsRep1 TReg-Act 8w H adult-8wks TReg-Activated DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002919 2919 GSM1003834 Stam UW-m DS20149 Hotspot-v5.2 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTregaC57bl6MAdult8wksHotspotsRep1 None Hotspots Adult 8 weeks Activated primary T regulatory cells, isolated ex vivo DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse ChIP-seq affinity zones identified using the HotSpot algorithm TReg-Activated 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTregC57bl6MAdult8wksHotspotsRep1 TReg 8w H adult-8wks TReg DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002911 2911 GSM1003826 Stam UW-m DS17864 Hotspot-v5.2 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTregC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Regulatory T cells CD4+,CD25+ DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm TReg 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTnaiveC57bl6MAdult8wksHotspotsRep2 T-Naive 8w H 2 adult-8wks T-Naive DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002910 2910 GSM1003825 Stam UW-m DS16171 Hotspot-v5.2 2 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTnaiveC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Naive T cells: CD4+, CD25- DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm T-Naive 8w C57BL/6 DNaseI DGF Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfTnaiveC57bl6MAdult8wksHotspotsRep1 T-Naive 8w H 1 adult-8wks T-Naive DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002910 2910 GSM1003825 Stam UW-m DS17080 Hotspot-v5.2 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfTnaiveC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Naive T cells: CD4+, CD25- DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm T-Naive 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfThymusC57bl6MAdult8wksHotspotsRep1 Thymus 8w H adult-8wks Thymus DnaseDgf ENCODE Mar 2012 Freeze 2011-12-18 2012-09-17 wgEncodeEM002912 2912 GSM1003827 Stam UW-m DS18819 Hotspot-v5.2 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfThymusC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Thymus DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Thymus 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfThelpaC57bl6MAdult8wksHotspotsRep1 THelp-Act 8w H adult-8wks THelper-Activated DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002918 2918 GSM1003833 Stam UW-m DS17070 Hotspot-v5.2 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfThelpaC57bl6MAdult8wksHotspotsRep1 None Hotspots Adult 8 weeks Activated primary CD4 effector cells, isolated ex vivo DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse ChIP-seq affinity zones identified using the HotSpot algorithm THelper-Activated 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfRetinaC57bl6MNew1daysHotspotsRep1 Retina 1day H newborn-1days Retina DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002917 2917 GSM1003832 Stam UW-m DS20004 Hotspot-v5.2 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfRetinaC57bl6MNew1daysHotspotsRep1 Pooled Hotspots Newborn 1 day Retina DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Retina Newborn 1 Day C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfNih3t3NihsMImmortalHotspotsRep1 NIH-3T3 Immt H immortalized NIH-3T3 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002916 2916 GSM1003831 Stam UW-m DS16900 Hotspot-v5.2 1 Illumina_HiSeq_2000 M NIH/Swiss wgEncodeUwDgfNih3t3NihsMImmortalHotspotsRep1 None Hotspots Immortal cells fibroblast DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. ChIP-seq affinity zones identified using the HotSpot algorithm NIH-3T3 Immortal NIH/Swiss DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfMelUknImmortalHotspotsRep1 MEL Immt H immortalized MEL DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002908 2908 GSM1003824 Stam UW-m DS13036 Hotspot-v5.2 1 Illumina_HiSeq_2000 M Unknown wgEncodeUwDgfMelUknImmortalHotspotsRep1 Pooled Hotspots Immortal cells Leukemia (K562 analog) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male Unknown strain origin Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm MEL Immortal DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfLungC57bl6MAdult8wksHotspotsRep1 Lung 8w H adult-8wks Lung DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002907 2907 GSM1003817 Stam UW-m DS14479 Hotspot-v5.2 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfLungC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Lung DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Lung 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfLiverC57bl6MAdult8wksHotspotsRep1 Liver 8w H adult-8wks Liver DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002906 2906 GSM1003818 Stam UW-m DS14605 Hotspot-v5.2 1 Illumina_GA2x M C57BL/6 wgEncodeUwDgfLiverC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Liver DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina Genome Analyzer IIx Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Liver 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfKidneyC57bl6MAdult8wksHotspotsRep1 Kidney 8w H adult-8wks Kidney DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002905 2905 GSM1003819 Stam UW-m DS13948 Hotspot-v5.2 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfKidneyC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Kidney DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Kidney 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfHeartC57bl6MAdult8wksHotspotsRep1 Heart 8w H adult-8wks Heart DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002904 2904 GSM1003820 Stam UW-m DS18138 Hotspot-v5.2 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfHeartC57bl6MAdult8wksHotspotsRep1 Individual Hotspots Adult 8 weeks Heart DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual ChIP-seq affinity zones identified using the HotSpot algorithm Heart 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfEscj7129s1ME0HotspotsRep1 ES-CJ7 E0 H E0 ES-CJ7 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002915 2915 GSM1003830 Stam UW-m DS13320 Hotspot-v5.2 1 Illumina_HiSeq_2000 M 129S1/SVImJ wgEncodeUwDgfEscj7129s1ME0HotspotsRep1 None Hotspots Embryonic day 0 (stem cell) ES-cells were originally isolated from 129S1/SVImJ mice by Swiatek PJ et al. in 1993 ("Perinatal lethality and defects in hindbrain development in mice homozygous for a targeted mutation of the zinc finger gene Krox20". Swiatek PJ, Gridley T. Genes Dev. 1993 Nov,7(11):2071-84.) DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male Control inbred strain of the steel-derived ES cells. ChIP-seq affinity zones identified using the HotSpot algorithm ES-CJ7 E0 129S1/SVImJ DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksHotspotsRep1 Bcell CD43- 8w H adult-8wks B-cell_(CD43-) DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002903 2903 GSM1003813 Stam UW-m DS17866 Hotspot-v5.2 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks mouse spleen B cells, CD43-,CD11b- DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm B-cell (CD43-) 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksHotspotsRep1 Bcell CD19+ 8w H adult-8wks B-cell_(CD19+) DnaseDgf ENCODE Mar 2012 Freeze 2012-01-18 2011-12-17 2012-09-17 wgEncodeEM002902 2902 GSM1003814 Stam UW-m DS16168 Hotspot-v5.2 1 Illumina_HiSeq_2000 M C57BL/6 wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks B Cell , CD19+ DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm B-cell (CD19+) 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgfA20BalbcannMImmortalHotspotsRep1 A20 Immt H immortalized A20 DnaseDgf ENCODE Jul 2012 Freeze 2012-05-01 2013-01-30 wgEncodeEM002914 2914 GSM1003829 Stam UW-m DS16695 Hotspot-v5.2 1 Illumina_HiSeq_2000 M BALB/cAnN wgEncodeUwDgfA20BalbcannMImmortalHotspotsRep1 None Hotspots Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male ccMyeloma high incidence H2d ChIP-seq affinity zones identified using the HotSpot algorithm A20 Immortal BALB/cAnN DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgf416bB6d2f1jImmortalHotspotsRep1 416B Immt H immortalized 416B DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-17 wgEncodeEM002901 2901 GSM1003815 Stam UW-m DS14099 Hotspot-v5.2 1 Illumina_HiSeq_2000 M B6D2F1/J wgEncodeUwDgf416bB6d2f1jImmortalHotspotsRep1 Pooled Hotspots Immortal cells myeloid progenitor cells, CD34+ DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina HiSeq 2000 Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm 416B Immortal B6D2F1/J DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDgf3134RiiiMImmortalHotspotsRep1 3134 Immt H immortalized 3134 DnaseDgf ENCODE Mar 2012 Freeze 2011-12-17 2012-09-16 wgEncodeEM002900 2900 GSM1003816 Stam UW-m DS8497 Hotspot-v5.2 1 Illumina_GA2x M RIII wgEncodeUwDgf3134RiiiMImmortalHotspotsRep1 None Hotspots Immortal cells Mammary DNase Digital Footprinting Stamatoyannopoulous Stamatoyannopoulous - University of Washington Illumina Genome Analyzer IIx Male High mammary tumor incidence in unfostered substrains. ChIP-seq affinity zones identified using the HotSpot algorithm 3134 Immortal RIII DNaseI DGF Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase UW DNaseI HS GSE37074 DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington Expression and Regulation Description This track was produced as part of the mouse ENCODE Project. It shows DNaseI sensitivity measured genome-wide in mouse tissues and cell lines using the Digital DNaseI methodology (see below), and DNaseI hypersensitive sites. DNaseI has long been used to map general chromatin accessibility and DNaseI hypersensitivity is a universal feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include enhancers, insulators, promoters, locus control regions and novel elements. For each experiment (tissue/cell type), this track shows DNaseI sensitivity as a continuous function using sequencing tag density (Signal), and discrete loci of DNaseI sensitive zones (HotSpots) and hypersensitive sites (Peaks). 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. This track contains the following views: HotSpots DNaseI sensitive zones identified using the HotSpot algorithm. Peaks DNaseI hypersensitive sites (DHSs) identified as signal peaks within FDR 1.0% hypersensitive zones. Signal The density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). DNaseI sensitivity is shown as the absolute density of in vivo cleavage sites across the genome mapped using the Digital DNaseI methodology (see below). Data have been normalized to 25 million reads per cell type. 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. Fresh tissues were harvested from mice and the nuclei prepared according to the tissue-appropriate protocol. Digital DNaseI was performed by DNaseI digestion of intact nuclei, isolating DNaseI 'double-hit' fragments as described in Sabo et al. (2006), and direct sequencing of fragment ends (which correspond to in vivo DNaseI cleavage sites) using the Illumina IIx (and Illumina HiSeq by early 2011) platform (36 bp reads). Uniquely-mapping high-quality reads were mapped to the genome using Bowtie. DNaseI sensitivity is directly reflected in raw tag density, 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). DNaseI sensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). False discovery rate thresholds of 1.0% (FDR 1.0%) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely-mapping 36mers. DNaseI hypersensitive sites (DHSs or Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm (I-max). Verification Data were verified by sequencing biological replicates displaying correlation coefficient &gt; 0.9. Release Notes This is Release 2 (September 2012) of this track. It adds 32 new experiments including 22 new cell lines and 4 new treatments. Credits These data were generated by the UW ENCODE group. Contact: Richard Sandstrom References John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet. 2011 Mar;43(3):264-8. 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. Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods. 2006 Jul;3(7):511-8. 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. 
wgEncodeUwDnaseViewRawSignal Signal DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0SigRep2 ZhBTc4 S 2 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001735 1735 GSM1014169 Stam UW-m WindowDensity-bin20-win+/-75 2 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0SigRep2 None Signal Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ZhBTc4 DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0SigRep1V2 ZhBTc4 S 1 E0 ZhBTc4 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2011-05-06 2012-02-06 wgEncodeEM001735 1735 GSM1014169 Stam UW-m DS17616 WindowDensity-bin20-win+/-75 1 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0SigRep1V2 None Signal Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ZhBTc4 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0Diffb6hSigRep2 ZhBTc4 dPB 6 S 2 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003407 3407 GSM1014150 Stam UW-m DS15860 WindowDensity-bin20-win+/-75 2 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0Diffb6hSigRep2 None diffProtB_6hr Signal Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 6 hours. Doxycycline added to a final concentration of 100 ng/ml. (Stam) Signal ZhBTc4 diffProtB 6 hr DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0Diffb6hSigRep1 ZhBTc4 dPB 6 S 1 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003407 3407 GSM1014150 Stam UW-m DS15236 WindowDensity-bin20-win+/-75 1 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0Diffb6hSigRep1 None diffProtB_6hr Signal Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 6 hours. Doxycycline added to a final concentration of 100 ng/ml. (Stam) Signal ZhBTc4 diffProtB 6 hr DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0Diffb24hSigRep2 ZhBTc4 dPB 24 S 2 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003406 3406 GSM1014152 Stam UW-m DS15299 WindowDensity-bin20-win+/-75 2 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0Diffb24hSigRep2 None diffProtB_24hr Signal Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 24 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam) Signal ZhBTc4 diffProtB 24 hr DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0Diffb24hSigRep1 ZhBTc4 dPB 24 S 1 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003406 3406 GSM1014152 Stam UW-m DS17562 WindowDensity-bin20-win+/-75 1 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0Diffb24hSigRep1 None diffProtB_24hr Signal Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 24 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam) Signal ZhBTc4 diffProtB 24 hr DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6ME18halfSigRep2 Brain E18.5 S 2 E18.5 WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM003396 3396 GSM1014184 Stam UW-m DS15269 WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6ME18halfSigRep2 Pooled Signal Embryonic day 18.5 Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Whole Brain Embryonic Day 18.5 DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6ME18halfSigRep1 Brain E18.5 S 1 E18.5 WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2011-12-15 2012-09-15 wgEncodeEM003396 3396 GSM1014184 Stam UW-m DS19690 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6ME18halfSigRep1 Pooled Signal Embryonic day 18.5 Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Whole Brain Embryonic Day 18.5 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6ME14halfSigRep2 Brain E14.5 S 2 E14.5 WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2010-07-27 2011-04-26 wgEncodeEM001726 1726 GSM1014197 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6ME14halfSigRep2 Individual Signal Embryonic day 14.5 Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Whole Brain Embryonic Day 14.5 DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6ME14halfSigRep1 Brain E14.5 S 1 E14.5 WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001726 1726 GSM1014197 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6ME14halfSigRep1 Individual Signal Embryonic day 14.5 Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Whole Brain Embryonic Day 14.5 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6MAdult8wksSigRep2 Brain A8w S 2 adult-8wks WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001729 1729 GSM1014151 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6MAdult8wksSigRep2 Individual Signal Adult 8 weeks Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Whole Brain Adult 8 Weeks DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6MAdult8wksSigRep1 Brain A8w S 1 adult-8wks WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001729 1729 GSM1014151 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6MAdult8wksSigRep1 Individual Signal Adult 8 weeks Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Whole Brain Adult 8 Weeks DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTregaC57bl6MAdult8wksSigRep2 TReg-Act S 2 adult-8wks TReg-Activated DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003404 3404 GSM1014200 Stam UW-m DS17077 WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseTregaC57bl6MAdult8wksSigRep2 None Signal Adult 8 weeks Activated primary T regulatory cells, isolated ex vivo DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Signal TReg-Activated DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTregaC57bl6MAdult8wksSigRep1 TReg-Act S 1 adult-8wks TReg-Activated DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003404 3404 GSM1014200 Stam UW-m DS20149 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseTregaC57bl6MAdult8wksSigRep1 None Signal Adult 8 weeks Activated primary T regulatory cells, isolated ex vivo DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Signal TReg-Activated DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTregC57bl6MAdult8wksSigRep2 TReg S 2 adult-8wks TReg DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001732 1732 GSM1014148 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseTregC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Regulatory T cells CD4+,CD25+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal TReg DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTregC57bl6MAdult8wksSigRep1 TReg S 1 adult-8wks TReg DnaseSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001732 1732 GSM1014148 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseTregC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Regulatory T cells CD4+,CD25+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal TReg DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseThymusC57bl6MAdult8wksSigRep2 Thymus S 2 adult-8wks Thymus DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM003395 3395 GSM1014185 Stam UW-m DS18890 WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseThymusC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Thymus DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Thymus DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseThymusC57bl6MAdult8wksSigRep1 Thymus S 1 adult-8wks Thymus DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM003395 3395 GSM1014185 Stam UW-m DS18819 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseThymusC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Thymus DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Thymus DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseThelpaC57bl6MAdult8wksSigRep2 THelper-Act S 2 adult-8wks THelper-Activated DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003403 3403 GSM1014149 Stam UW-m DS18848 WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseThelpaC57bl6MAdult8wksSigRep2 None Signal Adult 8 weeks Activated primary CD4 effector cells, isolated ex vivo DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Signal THelper-Activated DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseThelpaC57bl6MAdult8wksSigRep1 THelper-Act S 1 adult-8wks THelper-Activated DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003403 3403 GSM1014149 Stam UW-m DS17070 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseThelpaC57bl6MAdult8wksSigRep1 None Signal Adult 8 weeks Activated primary CD4 effector cells, isolated ex vivo DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Signal THelper-Activated DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTnaiveC57bl6MAdult8wksSigRep2 T-Naive S 2 adult-8wks T-Naive DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001725 1725 GSM1014192 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseTnaiveC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Naive T cells: CD4+, CD25- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal T-Naive DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTnaiveC57bl6MAdult8wksSigRep1 T-Naive S 1 adult-8wks T-Naive DnaseSeq ENCODE Mar 2012 Freeze 2011-04-18 2012-01-18 wgEncodeEM001725 1725 GSM1014192 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseTnaiveC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Naive T cells: CD4+, CD25- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal T-Naive DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseSpleenC57bl6MAdult8wksSigRep2 Spleen S 2 adult-8wks Spleen DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM003394 3394 GSM1014182 Stam UW-m DS18884 WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseSpleenC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Spleen DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Spleen DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseSpleenC57bl6MAdult8wksSigRep1 Spleen S 1 adult-8wks Spleen DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM003394 3394 GSM1014182 Stam UW-m DS18870 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseSpleenC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Spleen DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Spleen DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksSigRep2 Sk Muscle S 2 adult-8wks SkMuscle DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-19 2012-09-19 wgEncodeEM003399 3399 GSM1014189 Stam UW-m DS18892 WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Skeletal Muscle DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Skeletal Muscle DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksSigRep1 Sk Muscle S 1 adult-8wks SkMuscle DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-19 2012-09-19 wgEncodeEM003399 3399 GSM1014189 Stam UW-m DS18130 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Skeletal Muscle DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Skeletal Muscle DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseRetinaC57bl6MNew1daysSigRep1 Retina N1d S 1 newborn-1days Retina DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-20 2012-09-20 wgEncodeEM003400 3400 GSM1014188 Stam UW-m DS20004 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseRetinaC57bl6MNew1daysSigRep1 Pooled Signal Newborn 1 day Retina DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Retina Newborn 1 Day DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseRetinaC57bl6MAdult8wksSigRep1 Retina A8w S 1 adult-8wks Retina DnaseSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM003402 3402 GSM1014175 Stam UW-m DS19060 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseRetinaC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Retina DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Retina Adult 8 Weeks DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseRetinaC57bl6MAdult1wksSigRep1 Retina A1w S 1 adult-1wks Retina DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-19 2012-09-19 wgEncodeEM003398 3398 GSM1014198 Stam UW-m DS20000 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseRetinaC57bl6MAdult1wksSigRep1 Pooled Signal Adult 1 week Retina DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Retina Adult 1 week DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnasePatskiSpbl6MImmortalSigRep2 Patski S 2 immortalized Patski DnaseSeq ENCODE Mar 2012 Freeze 2011-05-10 2012-02-10 wgEncodeEM001736 1736 GSM1014171 Stam UW-m WindowDensity-bin20-win+/-75 2 M Spretus.BL6-Xist wgEncodeUwDnasePatskiSpbl6MImmortalSigRep2 None Signal Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. Signal Patski DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnasePatskiSpbl6MImmortalSigRep1 Patski S 1 immortalized Patski DnaseSeq ENCODE Mar 2012 Freeze 2011-05-10 2012-02-10 wgEncodeEM001736 1736 GSM1014171 Stam UW-m WindowDensity-bin20-win+/-75 1 M Spretus.BL6-Xist wgEncodeUwDnasePatskiSpbl6MImmortalSigRep1 None Signal Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. Signal Patski DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseNih3t3NihsMImmortalSigRep2 NIH-3T3 S 2 immortalized NIH-3T3 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001936 1936 GSM1014177 Stam UW-m WindowDensity-bin20-win+/-75 2 M NIH/Swiss wgEncodeUwDnaseNih3t3NihsMImmortalSigRep2 None Signal Immortal cells fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Signal NIH-3T3 DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseNih3t3NihsMImmortalSigRep1 NIH-3T3 S 1 immortalized NIH-3T3 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM001936 1936 GSM1014177 Stam UW-m DS16900 WindowDensity-bin20-win+/-75 1 M NIH/Swiss wgEncodeUwDnaseNih3t3NihsMImmortalSigRep1 Pooled Signal Immortal cells fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Tissue obtained from pooling samples from various sample organisms Signal NIH-3T3 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalSigRep2 mG/ER S 2 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003405 3405 GSM1014176 Stam UW-m DS15395 WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalSigRep2 None Signal Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Signal mG/ER DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalSigRep1 mG/ER S 1 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003405 3405 GSM1014176 Stam UW-m DS15400 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalSigRep1 None Signal Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Signal mG/ER DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalDiffc48hSigRep2 mG/ER dPC 48 S 2 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003409 3409 GSM1014180 Stam UW-m DS15415 WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalDiffc48hSigRep2 None diffProtC_48hr Signal Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse 48 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) Signal mG/ER diffProtC 48 hr DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalDiffc48hSigRep1 mG/ER dPC 48 S 1 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003409 3409 GSM1014180 Stam UW-m DS15420 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalDiffc48hSigRep1 None diffProtC_48hr Signal Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse 48 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) Signal mG/ER diffProtC 48 hr DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalDiffc24hSigRep2 mG/ER dPC 24 S 2 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003408 3408 GSM1014181 Stam UW-m DS15405 WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalDiffc24hSigRep2 None diffProtC_24hr Signal Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse 24 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) Signal mG/ER diffProtC 24 hr DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalDiffc24hSigRep1 mG/ER dPC 24 S 1 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003408 3408 GSM1014181 Stam UW-m DS15410 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalDiffc24hSigRep1 None diffProtC_24hr Signal Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse 24 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) Signal mG/ER diffProtC 24 hr DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMesodermCd1ME11halfSigRep2 Mesoderm S 2 E11.5 Mesoderm DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001935 1935 GSM1014178 Stam UW-m WindowDensity-bin20-win+/-75 2 M CD-1 wgEncodeUwDnaseMesodermCd1ME11halfSigRep2 Pooled Signal Embryonic day 11.5 axial somatic and lateral plate mesoderm from eviscerated headless, limbless embryos DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Signal Mesoderm DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMesodermCd1ME11halfSigRep1 Mesoderm S 1 E11.5 Mesoderm DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001935 1935 GSM1014178 Stam UW-m WindowDensity-bin20-win+/-75 1 M CD-1 wgEncodeUwDnaseMesodermCd1ME11halfSigRep1 Pooled Signal Embryonic day 11.5 axial somatic and lateral plate mesoderm from eviscerated headless, limbless embryos DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Signal Mesoderm DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMelC57bl6MAdult8wksSigRep2 MEL S 2 immortalized MEL DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001724 1724 GSM1014191 Stam UW-m WindowDensity-bin20-win+/-75 2 M Unknown wgEncodeUwDnaseMelC57bl6MAdult8wksSigRep2 Signal Immortal cells Leukemia (K562 analog) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin Signal MEL DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMelC57bl6MAdult8wksSigRep1 MEL S 1 immortalized MEL DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001724 1724 GSM1014191 Stam UW-m WindowDensity-bin20-win+/-75 1 M Unknown wgEncodeUwDnaseMelC57bl6MAdult8wksSigRep1 Signal Immortal cells Leukemia (K562 analog) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin Signal MEL DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLungC57bl6MAdult8wksSigRep2 Lung S 2 adult-8wks Lung DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001723 1723 GSM1014194 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseLungC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Lung DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Lung DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLungC57bl6MAdult8wksSigRep1 Lung S 1 adult-8wks Lung DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001723 1723 GSM1014194 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseLungC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Lung DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Lung DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiver129dlcrME14halfSigRep2 Livr 1D E14.5 S 2 E14.5 Liver DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003418 3418 GSM1014161 Stam UW-m DS19531 WindowDensity-bin20-win+/-75 2 M 129.DLCR/DLCR wgEncodeUwDnaseLiver129dlcrME14halfSigRep2 Pooled Signal Embryonic day 14.5 Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male 129 strain mouse with homozygous deletion of the beta-globin LCR region, see Bender et. al. (2000). Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region. Tissue obtained from pooling samples from various sample organisms Signal Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiver129dlcrME14halfSigRep1 Livr 1D E14.5 S 1 E14.5 Liver DnaseSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEM003418 3418 GSM1014161 Stam UW-m DS19241 WindowDensity-bin20-win+/-75 1 M 129.DLCR/DLCR wgEncodeUwDnaseLiver129dlcrME14halfSigRep1 Pooled Signal Embryonic day 14.5 Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male 129 strain mouse with homozygous deletion of the beta-globin LCR region, see Bender et. al. (2000). Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region. Tissue obtained from pooling samples from various sample organisms Signal Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiverS129ME14halfSigRep1 Livr 1 E14.5 S 1 E14.5 Liver DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003419 3419 GSM1014162 Stam UW-m DS19246 WindowDensity-bin20-win+/-75 1 M 129 wgEncodeUwDnaseLiverS129ME14halfSigRep1 Pooled Signal Embryonic day 14.5 Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Strain 129, has widely available embryonic stem cells Tissue obtained from pooling samples from various sample organisms Signal Liver 129 Embryonic Day 14.5 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiverC57bl6ME14halfSigRep1 Livr C E14.5 S 1 E14.5 Liver DnaseSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM003401 3401 GSM1014183 Stam UW-m DS20666 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseLiverC57bl6ME14halfSigRep1 Pooled Signal Embryonic day 14.5 Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Liver C57BL/6 Embryonic Day 14.5 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep2 Livr C A8w S 2 adult-8wks Liver DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001720 1720 GSM1014195 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Liver C57BL/6 Adult 8 Weeks DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep1 Livr C A8w S 1 adult-8wks Liver DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-23 wgEncodeEM001720 1720 GSM1014195 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Liver C57BL/6 Adult 8 Weeks DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLgintC57bl6MAdult8wksSigRep2 Lg Intestine S 2 adult-8wks LgIntestine DnaseSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM003397 3397 GSM1014186 Stam UW-m DS18784 WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseLgintC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Large Intestine DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Large Intestine DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLgintC57bl6MAdult8wksSigRep1 Lg Intestine S 1 adult-8wks LgIntestine DnaseSeq ENCODE Mar 2012 Freeze 2011-12-19 2012-09-19 wgEncodeEM003397 3397 GSM1014186 Stam UW-m DS19140 WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseLgintC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Large Intestine DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Large Intestine DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseKidneyC57bl6MAdult8wksSigRep2 Kidney S 2 adult-8wks Kidney DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001722 1722 GSM1014193 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseKidneyC57bl6MAdult8wksSigRep2 Individual Signal Adult 8 weeks Kidney DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Kidney DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseKidneyC57bl6MAdult8wksSigRep1 Kidney S 1 adult-8wks Kidney DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001722 1722 GSM1014193 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseKidneyC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Kidney DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Kidney DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHlbudCd1ME11halfSigRep2 Hind Limb Bud S 2 E11.5 HindlimbBud DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001934 1934 GSM1014179 Stam UW-m WindowDensity-bin20-win+/-75 2 M CD-1 wgEncodeUwDnaseHlbudCd1ME11halfSigRep2 Pooled Signal Embryonic day 11.5 embryo hindlimb buds DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Signal Hind Limb Bud DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHlbudCd1ME11halfSigRep1 Hind Limb Bud S 1 E11.5 HindlimbBud DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001934 1934 GSM1014179 Stam UW-m WindowDensity-bin20-win+/-75 1 M CD-1 wgEncodeUwDnaseHlbudCd1ME11halfSigRep1 Pooled Signal Embryonic day 11.5 embryo hindlimb buds DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Signal Hind Limb Bud DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHeartC57bl6MAdult8wksSigRep2 Heart S 2 adult-8wks Heart DnaseSeq ENCODE Mar 2012 Freeze 2011-12-15 2012-09-15 wgEncodeEM001730 1730 GSM1014166 Stam UW-m DS18138 WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseHeartC57bl6MAdult8wksSigRep2 Individual Signal Adult 8 weeks Heart DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Heart DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHeartC57bl6MAdult8wksSigRep1 Heart S 1 adult-8wks Heart DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001730 1730 GSM1014166 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseHeartC57bl6MAdult8wksSigRep1 Individual Signal Adult 8 weeks Heart DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Heart DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHlembryoCd1ME11halfSigRep2 Headless Emb S 2 E11.5 HeadlessEmbryo DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001933 1933 GSM1014172 Stam UW-m WindowDensity-bin20-win+/-75 2 M CD-1 wgEncodeUwDnaseHlembryoCd1ME11halfSigRep2 Pooled Signal Embryonic day 11.5 Whole embryos with heads removed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Signal Headless Embryo DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHlembryoCd1ME11halfSigRep1 Headless Emb S 1 E11.5 HeadlessEmbryo DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEM001933 1933 GSM1014172 Stam UW-m DS17129 WindowDensity-bin20-win+/-75 1 M CD-1 wgEncodeUwDnaseHlembryoCd1ME11halfSigRep1 Pooled Signal Embryonic day 11.5 Whole embryos with heads removed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Signal Headless Embryo DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseGfatC57bl6MAdult8wksSigRep2 Gen Fat Pad S 2 adult-8wks GenitalFatPad DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001932 1932 GSM1014173 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseGfatC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Genital Adipose tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Genital Fat Pad DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseGfatC57bl6MAdult8wksSigRep1 Gen Fat Pad S 1 adult-8wks GenitalFatPad DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001932 1932 GSM1014173 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseGfatC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Genital Adipose tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Genital Fat Pad DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFlbudCd1ME11halfSigRep2 Fore Limb Bud S 2 E11.5 ForelimbBud DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001931 1931 GSM1014174 Stam UW-m WindowDensity-bin20-win+/-75 2 M CD-1 wgEncodeUwDnaseFlbudCd1ME11halfSigRep2 Pooled Signal Embryonic day 11.5 embryo forelimb buds DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Signal Fore Limb Bud DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFlbudCd1ME11halfSigRep1 Fore Limb Bud S 1 E11.5 ForelimbBud DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001931 1931 GSM1014174 Stam UW-m WindowDensity-bin20-win+/-75 1 M CD-1 wgEncodeUwDnaseFlbudCd1ME11halfSigRep1 Pooled Signal Embryonic day 11.5 embryo forelimb buds DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Signal Fore Limb Bud DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFibroblastC57bl6MAdult8wksSigRep2 Fibroblast S 2 adult-8wks Fibroblast DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-23 wgEncodeEM001719 1719 GSM1014199 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseFibroblastC57bl6MAdult8wksSigRep2 Signal Adult 8 weeks Fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Signal Fibroblast DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFibroblastC57bl6MAdult8wksSigRep1 Fibroblast S 1 adult-8wks Fibroblast DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-23 wgEncodeEM001719 1719 GSM1014199 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseFibroblastC57bl6MAdult8wksSigRep1 Signal Adult 8 weeks Fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Signal Fibroblast DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFatC57bl6MAdult8wksSigRep2 Fat Pad S 2 adult-8wks FatPad DnaseSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001731 1731 GSM1014165 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseFatC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Adipose tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Fat Pad DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFatC57bl6MAdult8wksSigRep1 Fat Pad S 1 adult-8wks FatPad DnaseSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001731 1731 GSM1014165 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseFatC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Adipose tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Fat Pad DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEsww6koUknME0SigRep2 ES-WW6 F1KO S 2 E0 ES-WW6_F1KO DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEM003411 3411 GSM1014160 Stam UW-m DS18365 WindowDensity-bin20-win+/-75 2 M Unknown wgEncodeUwDnaseEsww6koUknME0SigRep2 None Signal Embryonic day 0 (stem cell) Histone H1c, H1d, H1e triple null mouse embryonic stem cell line derived from ES-WW6 cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin Signal ES-WW6 F1KO DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEsww6koUknME0SigRep1 ES-WW6 F1KO S 1 E0 ES-WW6_F1KO DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEM003411 3411 GSM1014160 Stam UW-m DS17063 WindowDensity-bin20-win+/-75 1 M Unknown wgEncodeUwDnaseEsww6koUknME0SigRep1 None Signal Embryonic day 0 (stem cell) Histone H1c, H1d, H1e triple null mouse embryonic stem cell line derived from ES-WW6 cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin Signal ES-WW6 F1KO DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEsww6UknME0SigRep2 ES-WW6 S 2 E0 ES-WW6 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEM003410 3410 GSM1014159 Stam UW-m DS17613 WindowDensity-bin20-win+/-75 2 M Unknown wgEncodeUwDnaseEsww6UknME0SigRep2 None Signal Embryonic day 0 (stem cell) ES-cells isolated from mix of ~20% C57/B6J, ~75% 129/Sv and ~5% SJL strains DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin Signal ES-WW6 DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEsww6UknME0SigRep1 ES-WW6 S 1 E0 ES-WW6 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEM003410 3410 GSM1014159 Stam UW-m DS17060 WindowDensity-bin20-win+/-75 1 M Unknown wgEncodeUwDnaseEsww6UknME0SigRep1 None Signal Embryonic day 0 (stem cell) ES-cells isolated from mix of ~20% C57/B6J, ~75% 129/Sv and ~5% SJL strains DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin Signal ES-WW6 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEse14129olaME0SigRep2 ES-E14 S 2 E0 ES-E14 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003417 3417 GSM1014154 Stam UW-m DS18505 WindowDensity-bin20-win+/-75 2 M 129/Ola wgEncodeUwDnaseEse14129olaME0SigRep2 None Signal Embryonic day 0 (stem cell) mouse embryonic stem cell line E14 DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEse14129olaME0SigRep1 ES-E14 S 1 E0 ES-E14 DnaseSeq ENCODE Jul 2012 Freeze 2012-05-01 2013-02-01 wgEncodeEM003417 3417 GSM1014154 Stam UW-m DS21450 WindowDensity-bin20-win+/-75 1 M 129/Ola wgEncodeUwDnaseEse14129olaME0SigRep1 None Signal Embryonic day 0 (stem cell) mouse embryonic stem cell line E14 DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Signal ES-E14 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEscj7S129ME0SigRep2 ES-CJ7 S 2 E0 ES-CJ7 DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001728 1728 GSM1014187 Stam UW-m WindowDensity-bin20-win+/-75 2 M 129S1/SVImJ wgEncodeUwDnaseEscj7S129ME0SigRep2 Signal Embryonic day 0 (stem cell) ES-cells were originally isolated from 129S1/SVImJ mice by Swiatek PJ et al. in 1993 ("Perinatal lethality and defects in hindbrain development in mice homozygous for a targeted mutation of the zinc finger gene Krox20". Swiatek PJ, Gridley T. Genes Dev. 1993 Nov,7(11):2071-84.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Control inbred strain of the steel-derived ES cells. Signal ES-CJ7 DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEscj7S129ME0SigRep1 ES-CJ7 S 1 E0 ES-CJ7 DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001728 1728 GSM1014187 Stam UW-m WindowDensity-bin20-win+/-75 1 M 129S1/SVImJ wgEncodeUwDnaseEscj7S129ME0SigRep1 Signal Embryonic day 0 (stem cell) ES-cells were originally isolated from 129S1/SVImJ mice by Swiatek PJ et al. in 1993 ("Perinatal lethality and defects in hindbrain development in mice homozygous for a targeted mutation of the zinc finger gene Krox20". Swiatek PJ, Gridley T. Genes Dev. 1993 Nov,7(11):2071-84.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Control inbred strain of the steel-derived ES cells. Signal ES-CJ7 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEpcpppCd1ME14halfSigRep1 EPC +++ S 1 E14.5 EPC_(CD117+_CD71+_TER119+) DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003412 3412 GSM1014157 Stam UW-m DS20999 WindowDensity-bin20-win+/-75 1 M CD-1 wgEncodeUwDnaseEpcpppCd1ME14halfSigRep1 None Signal Embryonic day 14.5 liver fraction CD117+,CD71+,TER119+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal EPC (CD117+,CD71+,TER119+) DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEpcppmCd1ME14halfSigRep1 EPC ++- S 1 E14.5 EPC_(CD117+_CD71+_TER119-) DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003413 3413 GSM1014158 Stam UW-m DS20994 WindowDensity-bin20-win+/-75 1 M CD-1 wgEncodeUwDnaseEpcppmCd1ME14halfSigRep1 None Signal Embryonic day 14.5 liver fraction CD117+,CD71+,TER119- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal EPC (CD117+,CD71+,TER119-) DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEpcpmmCd1ME14halfSigRep1 EPC +-- S 1 E14.5 EPC_(CD117+_CD71-_TER119-) DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003414 3414 GSM1014155 Stam UW-m DS20991 WindowDensity-bin20-win+/-75 1 M CD-1 wgEncodeUwDnaseEpcpmmCd1ME14halfSigRep1 None Signal Embryonic day 14.5 liver fraction CD117+,CD71-,TER119- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal EPC (CD117+,CD71-,TER119-) DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEpcmppCd1ME14halfSigRep1 EPC -++ S 1 E14.5 EPC_(CD117-_CD71+_TER119+) DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003415 3415 GSM1014156 Stam UW-m DS20937 WindowDensity-bin20-win+/-75 1 M CD-1 wgEncodeUwDnaseEpcmppCd1ME14halfSigRep1 None Signal Embryonic day 14.5 liver fraction CD117-,CD71+,TER119+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Signal EPC (CD117-,CD71+,TER119+) DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCh122a4bFImmortalSigRep2 CH12 S 2 immortalized CH12 DnaseSeq ENCODE Jul 2012 Freeze 2012-08-16 2013-05-16 wgEncodeEM003416 3416 GSM1014153 Stam UW-m DS22536 WindowDensity-bin20-win+/-75 2 F B10.H-2aH-4bp/Wts wgEncodeUwDnaseCh122a4bFImmortalSigRep2 None Signal Immortal cells B-cell lymphoma (GM12878 analog) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCh122a4bFImmortalSigRep1 CH12 S 1 immortalized CH12 DnaseSeq ENCODE Jul 2012 Freeze 2012-08-16 2013-05-16 wgEncodeEM003416 3416 GSM1014153 Stam UW-m DS22542 WindowDensity-bin20-win+/-75 1 F B10.H-2aH-4bp/Wts wgEncodeUwDnaseCh122a4bFImmortalSigRep1 None Signal Immortal cells B-cell lymphoma (GM12878 analog) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Signal CH12 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCerebrumC57bl6MAdult8wksSigRep2 Cerebrum S 2 adult-8wks Cerebrum DnaseSeq ENCODE Mar 2012 Freeze 2010-07-22 2011-04-22 wgEncodeEM001718 1718 GSM1014168 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseCerebrumC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Cerebrum DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cerebrum DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCerebrumC57bl6MAdult8wksSigRep1 Cerebrum S 1 adult-8wks Cerebrum DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-22 wgEncodeEM001718 1718 GSM1014168 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseCerebrumC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Cerebrum DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cerebrum DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCbellumC57bl6MAdult8wksSigRep2 Cerebellum S 2 adult-8wks Cerebellum DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001716 1716 GSM1014164 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseCbellumC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks Cerebellum DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cerebellum DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCerebellumC57bl6MAdult8wksSigRep1 Cerebellum S 1 adult-8wks Cerebellum DnaseSeq ENCODE Mar 2012 Freeze 2010-07-21 2011-04-20 wgEncodeEM001716 1716 GSM1014164 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseCerebellumC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks Cerebellum DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cerebellum DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksSigRep2 Bcell (CD43-) S 2 adult-8wks B-cell_(CD43-) DnaseSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001734 1734 GSM1014170 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksSigRep2 Pooled Signal Adult 8 weeks mouse spleen B cells, CD43-,CD11b- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal B-cell (CD43-) DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksSigRep1 Bcell (CD43-) S 1 adult-8wks B-cell_(CD43-) DnaseSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001734 1734 GSM1014170 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks mouse spleen B cells, CD43-,CD11b- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal B-cell (CD43-) DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksSigRep2 Bcell (CD19+) S 2 adult-8wks B-cell_(CD19+) DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001727 1727 GSM1014190 Stam UW-m WindowDensity-bin20-win+/-75 2 M C57BL/6 wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksSigRep2 Signal Adult 8 weeks B Cell , CD19+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Signal B-cell (CD19+) DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksSigRep1 Bcell (CD19+) S 1 adult-8wks B-cell_(CD19+) DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001727 1727 GSM1014190 Stam UW-m WindowDensity-bin20-win+/-75 1 M C57BL/6 wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksSigRep1 Pooled Signal Adult 8 weeks B Cell , CD19+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal B-cell (CD19+) DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseA20BalbcannMAdult8wksSigRep2 A20 S 2 immortalized A20 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-03 2012-02-03 wgEncodeEM001733 1733 GSM1014167 Stam UW-m WindowDensity-bin20-win+/-75 2 M BALB/cAnN wgEncodeUwDnaseA20BalbcannMAdult8wksSigRep2 None Signal Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male ccMyeloma high incidence H2d Signal A20 DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseA20BalbcannMAdult8wksSigRep1 A20 S 1 immortalized A20 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-03 2012-02-03 wgEncodeEM001733 1733 GSM1014167 Stam UW-m WindowDensity-bin20-win+/-75 1 M BALB/cAnN wgEncodeUwDnaseA20BalbcannMAdult8wksSigRep1 None Signal Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male ccMyeloma high incidence H2d Signal A20 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase416bC57bl6MAdult8wksSigRep2 416B S 2 immortalized 416B DnaseSeq ENCODE Mar 2012 Freeze 2010-07-22 2011-04-22 wgEncodeEM001717 1717 GSM1014163 Stam UW-m WindowDensity-bin20-win+/-75 2 M B6D2F1/J wgEncodeUwDnase416bC57bl6MAdult8wksSigRep2 Signal Immortal cells myeloid progenitor cells, CD34+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Signal 416B DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase416bC57bl6MAdult8wksSigRep1 416B S 1 immortalized 416B DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-22 wgEncodeEM001717 1717 GSM1014163 Stam UW-m WindowDensity-bin20-win+/-75 1 M B6D2F1/J wgEncodeUwDnase416bC57bl6MAdult8wksSigRep1 Signal Immortal cells myeloid progenitor cells, CD34+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Signal 416B DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase3134RiiiMImmortalSigRep2 3134 S 2 immortalized 3134 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-10 2012-02-10 wgEncodeEM001721 1721 GSM1014196 Stam UW-m WindowDensity-bin20-win+/-75 2 M RIII wgEncodeUwDnase3134RiiiMImmortalSigRep2 Signal Immortal cells Mammary DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male High mammary tumor incidence in unfostered substrains. Signal 3134 DNaseI HS Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase3134RiiiMImmortalSigRep1 3134 S 1 immortalized 3134 DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001721 1721 GSM1014196 Stam UW-m WindowDensity-bin20-win+/-75 1 M RIII wgEncodeUwDnase3134RiiiMImmortalSigRep1 Signal Immortal cells Mammary DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male High mammary tumor incidence in unfostered substrains. Signal 3134 DNaseI HS Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseViewPeaks Peaks DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0PkRep2 ZhBTc4 P 2 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001735 1735 GSM1014169 Stam UW-m lmax-v1.1 2 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0PkRep2 None Peaks Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ZhBTc4 DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0PkRep1V2 ZhBTc4 P 1 E0 ZhBTc4 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2011-05-06 2012-02-06 wgEncodeEM001735 1735 GSM1014169 Stam UW-m DS17616 lmax-v1.1 1 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0PkRep1V2 None Peaks Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ZhBTc4 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0Diffb6hPkRep2 ZhBTc4 dPB 6 P 2 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003407 3407 GSM1014150 Stam UW-m DS15860 lmax-v1.1 2 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0Diffb6hPkRep2 None diffProtB_6hr Peaks Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 6 hours. Doxycycline added to a final concentration of 100 ng/ml. (Stam) Regions of enriched signal in experiment ZhBTc4 diffProtB 6 hr DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0Diffb6hPkRep1 ZhBTc4 dPB 6 P 1 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003407 3407 GSM1014150 Stam UW-m DS15236 lmax-v1.1 1 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0Diffb6hPkRep1 None diffProtB_6hr Peaks Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 6 hours. Doxycycline added to a final concentration of 100 ng/ml. (Stam) Regions of enriched signal in experiment ZhBTc4 diffProtB 6 hr DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0Diffb24hPkRep2 ZhBTc4 dPB 24 P 2 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003406 3406 GSM1014152 Stam UW-m DS15299 lmax-v1.1 2 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0Diffb24hPkRep2 None diffProtB_24hr Peaks Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 24 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam) Regions of enriched signal in experiment ZhBTc4 diffProtB 24 hr DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0Diffb24hPkRep1 ZhBTc4 dPB 24 P 1 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003406 3406 GSM1014152 Stam UW-m DS17562 lmax-v1.1 1 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0Diffb24hPkRep1 None diffProtB_24hr Peaks Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 24 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam) Regions of enriched signal in experiment ZhBTc4 diffProtB 24 hr DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6ME18halfPkRep2 Brain E18.5 P 2 E18.5 WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM003396 3396 GSM1014184 Stam UW-m DS15269 lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6ME18halfPkRep2 Pooled Peaks Embryonic day 18.5 Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Whole Brain Embryonic Day 18.5 DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6ME18halfPkRep1 Brain E18.5 P 1 E18.5 WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2011-12-15 2012-09-15 wgEncodeEM003396 3396 GSM1014184 Stam UW-m DS19690 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6ME18halfPkRep1 Pooled Peaks Embryonic day 18.5 Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Whole Brain Embryonic Day 18.5 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6ME14halfPkRep2 Brain E14.5 P 2 E14.5 WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2010-07-27 2011-04-26 wgEncodeEM001726 1726 GSM1014197 Stam UW-m lmax-v1.0 2 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6ME14halfPkRep2 Individual Peaks Embryonic day 14.5 Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Whole Brain Embryonic Day 14.5 DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6ME14halfPkRep1 Brain E14.5 P 1 E14.5 WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001726 1726 GSM1014197 Stam UW-m lmax-v1.0 1 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6ME14halfPkRep1 Individual Peaks Embryonic day 14.5 Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Whole Brain Embryonic Day 14.5 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6MAdult8wksPkRep2 Brain A8w P 2 adult-8wks WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001729 1729 GSM1014151 Stam UW-m lmax-v1.0 2 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6MAdult8wksPkRep2 Individual Peaks Adult 8 weeks Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Whole Brain Adult 8 Weeks DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6MAdult8wksPkRep1 Brain A8w P 1 adult-8wks WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001729 1729 GSM1014151 Stam UW-m lmax-v1.0 1 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6MAdult8wksPkRep1 Individual Peaks Adult 8 weeks Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Whole Brain Adult 8 Weeks DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTregaC57bl6MAdult8wksPkRep2 TReg-Act P 2 adult-8wks TReg-Activated DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003404 3404 GSM1014200 Stam UW-m DS17077 lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseTregaC57bl6MAdult8wksPkRep2 None Peaks Adult 8 weeks Activated primary T regulatory cells, isolated ex vivo DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment TReg-Activated DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTregaC57bl6MAdult8wksPkRep1 TReg-Act P 1 adult-8wks TReg-Activated DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003404 3404 GSM1014200 Stam UW-m DS20149 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseTregaC57bl6MAdult8wksPkRep1 None Peaks Adult 8 weeks Activated primary T regulatory cells, isolated ex vivo DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment TReg-Activated DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTregC57bl6MAdult8wksPkRep2 TReg P 2 adult-8wks TReg DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001732 1732 GSM1014148 Stam UW-m lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseTregC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Regulatory T cells CD4+,CD25+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment TReg DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTregC57bl6MAdult8wksPkRep1 TReg P 1 adult-8wks TReg DnaseSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001732 1732 GSM1014148 Stam UW-m lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseTregC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Regulatory T cells CD4+,CD25+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment TReg DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseThymusC57bl6MAdult8wksPkRep2 Thymus P 2 adult-8wks Thymus DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM003395 3395 GSM1014185 Stam UW-m DS18890 lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseThymusC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Thymus DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Thymus DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseThymusC57bl6MAdult8wksPkRep1 Thymus P 1 adult-8wks Thymus DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM003395 3395 GSM1014185 Stam UW-m DS18819 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseThymusC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Thymus DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Thymus DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseThelpaC57bl6MAdult8wksPkRep2 THelper-Act P 2 adult-8wks THelper-Activated DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003403 3403 GSM1014149 Stam UW-m DS18848 lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseThelpaC57bl6MAdult8wksPkRep2 None Peaks Adult 8 weeks Activated primary CD4 effector cells, isolated ex vivo DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment THelper-Activated DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseThelpaC57bl6MAdult8wksPkRep1 THelper-Act P 1 adult-8wks THelper-Activated DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003403 3403 GSM1014149 Stam UW-m DS17070 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseThelpaC57bl6MAdult8wksPkRep1 None Peaks Adult 8 weeks Activated primary CD4 effector cells, isolated ex vivo DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment THelper-Activated DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTnaiveC57bl6MAdult8wksPkRep2 T-Naive P 2 adult-8wks T-Naive DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001725 1725 GSM1014192 Stam UW-m lmax-v1.0 2 M C57BL/6 wgEncodeUwDnaseTnaiveC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Naive T cells: CD4+, CD25- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment T-Naive DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTnaiveC57bl6MAdult8wksPkRep1 T-Naive P 1 adult-8wks T-Naive DnaseSeq ENCODE Mar 2012 Freeze 2011-04-18 2012-01-18 wgEncodeEM001725 1725 GSM1014192 Stam UW-m lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseTnaiveC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Naive T cells: CD4+, CD25- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment T-Naive DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseSpleenC57bl6MAdult8wksPkRep2 Spleen P 2 adult-8wks Spleen DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM003394 3394 GSM1014182 Stam UW-m DS18884 lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseSpleenC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Spleen DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Spleen DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseSpleenC57bl6MAdult8wksPkRep1 Spleen P 1 adult-8wks Spleen DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM003394 3394 GSM1014182 Stam UW-m DS18870 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseSpleenC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Spleen DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Spleen DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksPkRep2 Sk Muscle P 2 adult-8wks SkMuscle DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-19 2012-09-19 wgEncodeEM003399 3399 GSM1014189 Stam UW-m DS18892 lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Skeletal Muscle DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Skeletal Muscle DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksPkRep1 Sk Muscle P 1 adult-8wks SkMuscle DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-19 2012-09-19 wgEncodeEM003399 3399 GSM1014189 Stam UW-m DS18130 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Skeletal Muscle DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Skeletal Muscle DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseRetinaC57bl6MNew1daysPkRep1 Retina N1d P 1 newborn-1days Retina DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-20 2012-09-20 wgEncodeEM003400 3400 GSM1014188 Stam UW-m DS20004 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseRetinaC57bl6MNew1daysPkRep1 Pooled Peaks Newborn 1 day Retina DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Retina Newborn 1 Day DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseRetinaC57bl6MAdult8wksPkRep1 Retina A8w P 1 adult-8wks Retina DnaseSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM003402 3402 GSM1014175 Stam UW-m DS19060 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseRetinaC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Retina DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Retina Adult 8 Weeks DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseRetinaC57bl6MAdult1wksPkRep1 Retina A1w P 1 adult-1wks Retina DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-19 2012-09-19 wgEncodeEM003398 3398 GSM1014198 Stam UW-m DS20000 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseRetinaC57bl6MAdult1wksPkRep1 Pooled Peaks Adult 1 week Retina DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Retina Adult 1 week DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnasePatskiSpbl6MImmortalPkRep2 Patski P 2 immortalized Patski DnaseSeq ENCODE Mar 2012 Freeze 2011-05-10 2012-02-10 wgEncodeEM001736 1736 GSM1014171 Stam UW-m lmax-v1.1 2 M Spretus.BL6-Xist wgEncodeUwDnasePatskiSpbl6MImmortalPkRep2 None Peaks Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. Regions of enriched signal in experiment Patski DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnasePatskiSpbl6MImmortalPkRep1 Patski P 1 immortalized Patski DnaseSeq ENCODE Mar 2012 Freeze 2011-05-10 2012-02-10 wgEncodeEM001736 1736 GSM1014171 Stam UW-m lmax-v1.1 1 M Spretus.BL6-Xist wgEncodeUwDnasePatskiSpbl6MImmortalPkRep1 None Peaks Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. Regions of enriched signal in experiment Patski DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseNih3t3NihsMImmortalPkRep2 NIH-3T3 P 2 immortalized NIH-3T3 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001936 1936 GSM1014177 Stam UW-m lmax-v1.1 2 M NIH/Swiss wgEncodeUwDnaseNih3t3NihsMImmortalPkRep2 None Peaks Immortal cells fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Regions of enriched signal in experiment NIH-3T3 DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseNih3t3NihsMImmortalPkRep1 NIH-3T3 P 1 immortalized NIH-3T3 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM001936 1936 GSM1014177 Stam UW-m DS16900 lmax-v1.1 1 M NIH/Swiss wgEncodeUwDnaseNih3t3NihsMImmortalPkRep1 Pooled Peaks Immortal cells fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment NIH-3T3 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalPkRep2 mG/ER P 2 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003405 3405 GSM1014176 Stam UW-m DS15395 lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalPkRep2 None Peaks Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment mG/ER DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalPkRep1 mG/ER P 1 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003405 3405 GSM1014176 Stam UW-m DS15400 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalPkRep1 None Peaks Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment mG/ER DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalDiffc48hPkRep2 mG/ER dPC 48 P 2 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003409 3409 GSM1014180 Stam UW-m DS15415 lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalDiffc48hPkRep2 None diffProtC_48hr Peaks Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse 48 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) Regions of enriched signal in experiment mG/ER diffProtC 48 hr DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalDiffc48hPkRep1 mG/ER dPC 48 P 1 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003409 3409 GSM1014180 Stam UW-m DS15420 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalDiffc48hPkRep1 None diffProtC_48hr Peaks Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse 48 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) Regions of enriched signal in experiment mG/ER diffProtC 48 hr DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalDiffc24hPkRep2 mG/ER dPC 24 P 2 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003408 3408 GSM1014181 Stam UW-m DS15405 lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalDiffc24hPkRep2 None diffProtC_24hr Peaks Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse 24 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) Regions of enriched signal in experiment mG/ER diffProtC 24 hr DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalDiffc24hPkRep1 mG/ER dPC 24 P 1 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003408 3408 GSM1014181 Stam UW-m DS15410 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalDiffc24hPkRep1 None diffProtC_24hr Peaks Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse 24 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) Regions of enriched signal in experiment mG/ER diffProtC 24 hr DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMesodermCd1ME11halfPkRep2 Mesoderm P 2 E11.5 Mesoderm DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001935 1935 GSM1014178 Stam UW-m lmax-v1.1 2 M CD-1 wgEncodeUwDnaseMesodermCd1ME11halfPkRep2 Pooled Peaks Embryonic day 11.5 axial somatic and lateral plate mesoderm from eviscerated headless, limbless embryos DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Mesoderm DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMesodermCd1ME11halfPkRep1 Mesoderm P 1 E11.5 Mesoderm DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001935 1935 GSM1014178 Stam UW-m lmax-v1.1 1 M CD-1 wgEncodeUwDnaseMesodermCd1ME11halfPkRep1 Pooled Peaks Embryonic day 11.5 axial somatic and lateral plate mesoderm from eviscerated headless, limbless embryos DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Mesoderm DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMelC57bl6MAdult8wksPkRep2 MEL P 2 immortalized MEL DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001724 1724 GSM1014191 Stam UW-m lmax-v1.0 2 M Unknown wgEncodeUwDnaseMelC57bl6MAdult8wksPkRep2 Peaks Immortal cells Leukemia (K562 analog) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin Regions of enriched signal in experiment MEL DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMelC57bl6MAdult8wksPkRep1 MEL P 1 immortalized MEL DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001724 1724 GSM1014191 Stam UW-m lmax-v1.0 1 M Unknown wgEncodeUwDnaseMelC57bl6MAdult8wksPkRep1 Peaks Immortal cells Leukemia (K562 analog) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin Regions of enriched signal in experiment MEL DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLungC57bl6MAdult8wksPkRep2 Lung P 2 adult-8wks Lung DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001723 1723 GSM1014194 Stam UW-m lmax-v1.0 2 M C57BL/6 wgEncodeUwDnaseLungC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Lung DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Lung DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLungC57bl6MAdult8wksPkRep1 Lung P 1 adult-8wks Lung DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001723 1723 GSM1014194 Stam UW-m lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseLungC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Lung DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Lung DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiver129dlcrME14halfPkRep2 Livr 1D E14.5 P 2 E14.5 Liver DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003418 3418 GSM1014161 Stam UW-m DS19531 lmax-v1.1 2 M 129.DLCR/DLCR wgEncodeUwDnaseLiver129dlcrME14halfPkRep2 Pooled Peaks Embryonic day 14.5 Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male 129 strain mouse with homozygous deletion of the beta-globin LCR region, see Bender et. al. (2000). Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region. Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiver129dlcrME14halfPkRep1 Livr 1D E14.5 P 1 E14.5 Liver DnaseSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEM003418 3418 GSM1014161 Stam UW-m DS19241 lmax-v1.1 1 M 129.DLCR/DLCR wgEncodeUwDnaseLiver129dlcrME14halfPkRep1 Pooled Peaks Embryonic day 14.5 Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male 129 strain mouse with homozygous deletion of the beta-globin LCR region, see Bender et. al. (2000). Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region. Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiverS129ME14halfPkRep1 Livr 1 E14.5 P 1 E14.5 Liver DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003419 3419 GSM1014162 Stam UW-m DS19246 lmax-v1.1 1 M 129 wgEncodeUwDnaseLiverS129ME14halfPkRep1 Pooled Peaks Embryonic day 14.5 Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Strain 129, has widely available embryonic stem cells Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Liver 129 Embryonic Day 14.5 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiverC57bl6ME14halfPkRep1 Livr C E14.5 P 1 E14.5 Liver DnaseSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM003401 3401 GSM1014183 Stam UW-m DS20666 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseLiverC57bl6ME14halfPkRep1 Pooled Peaks Embryonic day 14.5 Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Liver C57BL/6 Embryonic Day 14.5 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep2 Livr C A8w P 2 adult-8wks Liver DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001720 1720 GSM1014195 Stam UW-m lmax-v1.0 2 M C57BL/6 wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Liver C57BL/6 Adult 8 Weeks DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep1 Livr C A8w P 1 adult-8wks Liver DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-23 wgEncodeEM001720 1720 GSM1014195 Stam UW-m lmax-v1.0 1 M C57BL/6 wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Liver C57BL/6 Adult 8 Weeks DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLgintC57bl6MAdult8wksPkRep2 Lg Intestine P 2 adult-8wks LgIntestine DnaseSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM003397 3397 GSM1014186 Stam UW-m DS18784 lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseLgintC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Large Intestine DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Large Intestine DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLgintC57bl6MAdult8wksPkRep1 Lg Intestine P 1 adult-8wks LgIntestine DnaseSeq ENCODE Mar 2012 Freeze 2011-12-19 2012-09-19 wgEncodeEM003397 3397 GSM1014186 Stam UW-m DS19140 lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseLgintC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Large Intestine DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Large Intestine DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseKidneyC57bl6MAdult8wksPkRep2 Kidney P 2 adult-8wks Kidney DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001722 1722 GSM1014193 Stam UW-m lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseKidneyC57bl6MAdult8wksPkRep2 Individual Peaks Adult 8 weeks Kidney DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Kidney DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseKidneyC57bl6MAdult8wksPkRep1 Kidney P 1 adult-8wks Kidney DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001722 1722 GSM1014193 Stam UW-m lmax-v1.0 1 M C57BL/6 wgEncodeUwDnaseKidneyC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Kidney DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Kidney DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHlbudCd1ME11halfPkRep2 Hind Limb Bud P 2 E11.5 HindlimbBud DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001934 1934 GSM1014179 Stam UW-m lmax-v1.1 2 M CD-1 wgEncodeUwDnaseHlbudCd1ME11halfPkRep2 Pooled Peaks Embryonic day 11.5 embryo hindlimb buds DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Hind Limb Bud DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHlbudCd1ME11halfPkRep1 Hind Limb Bud P 1 E11.5 HindlimbBud DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001934 1934 GSM1014179 Stam UW-m lmax-v1.1 1 M CD-1 wgEncodeUwDnaseHlbudCd1ME11halfPkRep1 Pooled Peaks Embryonic day 11.5 embryo hindlimb buds DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Hind Limb Bud DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHeartC57bl6MAdult8wksPkRep2 Heart P 2 adult-8wks Heart DnaseSeq ENCODE Mar 2012 Freeze 2011-12-15 2012-09-15 wgEncodeEM001730 1730 GSM1014166 Stam UW-m DS18138 lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseHeartC57bl6MAdult8wksPkRep2 Individual Peaks Adult 8 weeks Heart DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Heart DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHeartC57bl6MAdult8wksPkRep1 Heart P 1 adult-8wks Heart DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001730 1730 GSM1014166 Stam UW-m lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseHeartC57bl6MAdult8wksPkRep1 Individual Peaks Adult 8 weeks Heart DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Regions of enriched signal in experiment Heart DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHlembryoCd1ME11halfPkRep2 Headless Emb P 2 E11.5 HeadlessEmbryo DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001933 1933 GSM1014172 Stam UW-m lmax-v1.1 2 M CD-1 wgEncodeUwDnaseHlembryoCd1ME11halfPkRep2 Pooled Peaks Embryonic day 11.5 Whole embryos with heads removed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Headless Embryo DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHlembryoCd1ME11halfPkRep1 Headless Emb P 1 E11.5 HeadlessEmbryo DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEM001933 1933 GSM1014172 Stam UW-m DS17129 lmax-v1.1 1 M CD-1 wgEncodeUwDnaseHlembryoCd1ME11halfPkRep1 Pooled Peaks Embryonic day 11.5 Whole embryos with heads removed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Headless Embryo DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseGfatC57bl6MAdult8wksPkRep2 Gen Fat Pad P 2 adult-8wks GenitalFatPad DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001932 1932 GSM1014173 Stam UW-m lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseGfatC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Genital Adipose tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Genital Fat Pad DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseGfatC57bl6MAdult8wksPkRep1 Gen Fat Pad P 1 adult-8wks GenitalFatPad DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001932 1932 GSM1014173 Stam UW-m lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseGfatC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Genital Adipose tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Genital Fat Pad DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFlbudCd1ME11halfPkRep2 Fore Limb Bud P 2 E11.5 ForelimbBud DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001931 1931 GSM1014174 Stam UW-m lmax-v1.1 2 M CD-1 wgEncodeUwDnaseFlbudCd1ME11halfPkRep2 Pooled Peaks Embryonic day 11.5 embryo forelimb buds DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Fore Limb Bud DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFlbudCd1ME11halfPkRep1 Fore Limb Bud P 1 E11.5 ForelimbBud DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001931 1931 GSM1014174 Stam UW-m lmax-v1.1 1 M CD-1 wgEncodeUwDnaseFlbudCd1ME11halfPkRep1 Pooled Peaks Embryonic day 11.5 embryo forelimb buds DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Fore Limb Bud DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFibroblastC57bl6MAdult8wksPkRep2 Fibroblast P 2 adult-8wks Fibroblast DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-23 wgEncodeEM001719 1719 GSM1014199 Stam UW-m lmax-v1.0 2 M C57BL/6 wgEncodeUwDnaseFibroblastC57bl6MAdult8wksPkRep2 Peaks Adult 8 weeks Fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Fibroblast DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFibroblastC57bl6MAdult8wksPkRep1 Fibroblast P 1 adult-8wks Fibroblast DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-23 wgEncodeEM001719 1719 GSM1014199 Stam UW-m lmax-v1.0 1 M C57BL/6 wgEncodeUwDnaseFibroblastC57bl6MAdult8wksPkRep1 Peaks Adult 8 weeks Fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment Fibroblast DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFatC57bl6MAdult8wksPkRep2 Fat Pad P 2 adult-8wks FatPad DnaseSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001731 1731 GSM1014165 Stam UW-m lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseFatC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Adipose tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Fat Pad DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFatC57bl6MAdult8wksPkRep1 Fat Pad P 1 adult-8wks FatPad DnaseSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001731 1731 GSM1014165 Stam UW-m lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseFatC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Adipose tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Fat Pad DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEsww6koUknME0PkRep2 ES-WW6 F1KO P 2 E0 ES-WW6_F1KO DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEM003411 3411 GSM1014160 Stam UW-m DS18365 lmax-v1.1 2 M Unknown wgEncodeUwDnaseEsww6koUknME0PkRep2 None Peaks Embryonic day 0 (stem cell) Histone H1c, H1d, H1e triple null mouse embryonic stem cell line derived from ES-WW6 cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin Regions of enriched signal in experiment ES-WW6 F1KO DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEsww6koUknME0PkRep1 ES-WW6 F1KO P 1 E0 ES-WW6_F1KO DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEM003411 3411 GSM1014160 Stam UW-m DS17063 lmax-v1.1 1 M Unknown wgEncodeUwDnaseEsww6koUknME0PkRep1 None Peaks Embryonic day 0 (stem cell) Histone H1c, H1d, H1e triple null mouse embryonic stem cell line derived from ES-WW6 cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin Regions of enriched signal in experiment ES-WW6 F1KO DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEsww6UknME0PkRep2 ES-WW6 P 2 E0 ES-WW6 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEM003410 3410 GSM1014159 Stam UW-m DS17613 lmax-v1.1 2 M Unknown wgEncodeUwDnaseEsww6UknME0PkRep2 None Peaks Embryonic day 0 (stem cell) ES-cells isolated from mix of ~20% C57/B6J, ~75% 129/Sv and ~5% SJL strains DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin Regions of enriched signal in experiment ES-WW6 DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEsww6UknME0PkRep1 ES-WW6 P 1 E0 ES-WW6 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEM003410 3410 GSM1014159 Stam UW-m DS17060 lmax-v1.1 1 M Unknown wgEncodeUwDnaseEsww6UknME0PkRep1 None Peaks Embryonic day 0 (stem cell) ES-cells isolated from mix of ~20% C57/B6J, ~75% 129/Sv and ~5% SJL strains DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin Regions of enriched signal in experiment ES-WW6 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEse14129olaME0PkRep2 ES-E14 P 2 E0 ES-E14 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003417 3417 GSM1014154 Stam UW-m DS18505 lmax-v1.1 2 M 129/Ola wgEncodeUwDnaseEse14129olaME0PkRep2 None Peaks Embryonic day 0 (stem cell) mouse embryonic stem cell line E14 DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEse14129olaME0PkRep1 ES-E14 P 1 E0 ES-E14 DnaseSeq ENCODE Jul 2012 Freeze 2012-05-01 2013-02-01 wgEncodeEM003417 3417 GSM1014154 Stam UW-m DS21450 lmax-v1.1 1 M 129/Ola wgEncodeUwDnaseEse14129olaME0PkRep1 None Peaks Embryonic day 0 (stem cell) mouse embryonic stem cell line E14 DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Regions of enriched signal in experiment ES-E14 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEscj7S129ME0PkRep2 ES-CJ7 P 2 E0 ES-CJ7 DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001728 1728 GSM1014187 Stam UW-m lmax-v1.0 2 M 129S1/SVImJ wgEncodeUwDnaseEscj7S129ME0PkRep2 Peaks Embryonic day 0 (stem cell) ES-cells were originally isolated from 129S1/SVImJ mice by Swiatek PJ et al. in 1993 ("Perinatal lethality and defects in hindbrain development in mice homozygous for a targeted mutation of the zinc finger gene Krox20". Swiatek PJ, Gridley T. Genes Dev. 1993 Nov,7(11):2071-84.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Control inbred strain of the steel-derived ES cells. Regions of enriched signal in experiment ES-CJ7 DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEscj7S129ME0PkRep1 ES-CJ7 P 1 E0 ES-CJ7 DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001728 1728 GSM1014187 Stam UW-m lmax-v1.0 1 M 129S1/SVImJ wgEncodeUwDnaseEscj7S129ME0PkRep1 Peaks Embryonic day 0 (stem cell) ES-cells were originally isolated from 129S1/SVImJ mice by Swiatek PJ et al. in 1993 ("Perinatal lethality and defects in hindbrain development in mice homozygous for a targeted mutation of the zinc finger gene Krox20". Swiatek PJ, Gridley T. Genes Dev. 1993 Nov,7(11):2071-84.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Control inbred strain of the steel-derived ES cells. Regions of enriched signal in experiment ES-CJ7 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEpcpppCd1ME14halfPkRep1 EPC +++ P 1 E14.5 EPC_(CD117+_CD71+_TER119+) DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003412 3412 GSM1014157 Stam UW-m DS20999 lmax-v1.1 1 M CD-1 wgEncodeUwDnaseEpcpppCd1ME14halfPkRep1 None Peaks Embryonic day 14.5 liver fraction CD117+,CD71+,TER119+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment EPC (CD117+,CD71+,TER119+) DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEpcppmCd1ME14halfPkRep1 EPC ++- P 1 E14.5 EPC_(CD117+_CD71+_TER119-) DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003413 3413 GSM1014158 Stam UW-m DS20994 lmax-v1.1 1 M CD-1 wgEncodeUwDnaseEpcppmCd1ME14halfPkRep1 None Peaks Embryonic day 14.5 liver fraction CD117+,CD71+,TER119- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment EPC (CD117+,CD71+,TER119-) DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEpcpmmCd1ME14halfPkRep1 EPC +-- P 1 E14.5 EPC_(CD117+_CD71-_TER119-) DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003414 3414 GSM1014155 Stam UW-m DS20991 lmax-v1.1 1 M CD-1 wgEncodeUwDnaseEpcpmmCd1ME14halfPkRep1 None Peaks Embryonic day 14.5 liver fraction CD117+,CD71-,TER119- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment EPC (CD117+,CD71-,TER119-) DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEpcmppCd1ME14halfPkRep1 EPC -++ P 1 E14.5 EPC_(CD117-_CD71+_TER119+) DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003415 3415 GSM1014156 Stam UW-m DS20937 lmax-v1.1 1 M CD-1 wgEncodeUwDnaseEpcmppCd1ME14halfPkRep1 None Peaks Embryonic day 14.5 liver fraction CD117-,CD71+,TER119+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Regions of enriched signal in experiment EPC (CD117-,CD71+,TER119+) DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCh122a4bFImmortalPkRep2 CH12 P 2 immortalized CH12 DnaseSeq ENCODE Jul 2012 Freeze 2012-08-16 2013-05-16 wgEncodeEM003416 3416 GSM1014153 Stam UW-m DS22536 lmax-v1.1 2 F B10.H-2aH-4bp/Wts wgEncodeUwDnaseCh122a4bFImmortalPkRep2 None Peaks Immortal cells B-cell lymphoma (GM12878 analog) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCh122a4bFImmortalPkRep1 CH12 P 1 immortalized CH12 DnaseSeq ENCODE Jul 2012 Freeze 2012-08-16 2013-05-16 wgEncodeEM003416 3416 GSM1014153 Stam UW-m DS22542 lmax-v1.1 1 F B10.H-2aH-4bp/Wts wgEncodeUwDnaseCh122a4bFImmortalPkRep1 None Peaks Immortal cells B-cell lymphoma (GM12878 analog) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 Regions of enriched signal in experiment CH12 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCerebrumC57bl6MAdult8wksPkRep2 Cerebrum P 2 adult-8wks Cerebrum DnaseSeq ENCODE Mar 2012 Freeze 2010-07-22 2011-04-22 wgEncodeEM001718 1718 GSM1014168 Stam UW-m lmax-v1.0 2 M C57BL/6 wgEncodeUwDnaseCerebrumC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Cerebrum DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Cerebrum DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCerebrumC57bl6MAdult8wksPkRep1 Cerebrum P 1 adult-8wks Cerebrum DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-22 wgEncodeEM001718 1718 GSM1014168 Stam UW-m lmax-v1.0 1 M C57BL/6 wgEncodeUwDnaseCerebrumC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Cerebrum DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Cerebrum DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCbellumC57bl6MAdult8wksPkRep2 Cerebellum P 2 adult-8wks Cerebellum DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001716 1716 GSM1014164 Stam UW-m lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseCbellumC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks Cerebellum DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Cerebellum DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCerebellumC57bl6MAdult8wksPkRep1 Cerebellum P 1 adult-8wks Cerebellum DnaseSeq ENCODE Mar 2012 Freeze 2010-07-21 2011-04-20 wgEncodeEM001716 1716 GSM1014164 Stam UW-m lmax-v1.0 1 M C57BL/6 wgEncodeUwDnaseCerebellumC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks Cerebellum DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment Cerebellum DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksPkRep2 Bcell (CD43-) P 2 adult-8wks B-cell_(CD43-) DnaseSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001734 1734 GSM1014170 Stam UW-m lmax-v1.1 2 M C57BL/6 wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksPkRep2 Pooled Peaks Adult 8 weeks mouse spleen B cells, CD43-,CD11b- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment B-cell (CD43-) DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksPkRep1 Bcell (CD43-) P 1 adult-8wks B-cell_(CD43-) DnaseSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001734 1734 GSM1014170 Stam UW-m lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks mouse spleen B cells, CD43-,CD11b- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment B-cell (CD43-) DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksPkRep2 Bcell (CD19+) P 2 adult-8wks B-cell_(CD19+) DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001727 1727 GSM1014190 Stam UW-m lmax-v1.0 2 M C57BL/6 wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksPkRep2 Peaks Adult 8 weeks B Cell , CD19+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Regions of enriched signal in experiment B-cell (CD19+) DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksPkRep1 Bcell (CD19+) P 1 adult-8wks B-cell_(CD19+) DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001727 1727 GSM1014190 Stam UW-m lmax-v1.1 1 M C57BL/6 wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksPkRep1 Pooled Peaks Adult 8 weeks B Cell , CD19+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Regions of enriched signal in experiment B-cell (CD19+) DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseA20BalbcannMAdult8wksPkRep2 A20 P 2 immortalized A20 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-03 2012-02-03 wgEncodeEM001733 1733 GSM1014167 Stam UW-m lmax-v1.1 2 M BALB/cAnN wgEncodeUwDnaseA20BalbcannMAdult8wksPkRep2 None Peaks Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male ccMyeloma high incidence H2d Regions of enriched signal in experiment A20 DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseA20BalbcannMAdult8wksPkRep1 A20 P 1 immortalized A20 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-03 2012-02-03 wgEncodeEM001733 1733 GSM1014167 Stam UW-m lmax-v1.1 1 M BALB/cAnN wgEncodeUwDnaseA20BalbcannMAdult8wksPkRep1 None Peaks Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male ccMyeloma high incidence H2d Regions of enriched signal in experiment A20 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase416bC57bl6MAdult8wksPkRep2 416B P 2 immortalized 416B DnaseSeq ENCODE Mar 2012 Freeze 2010-07-22 2011-04-22 wgEncodeEM001717 1717 GSM1014163 Stam UW-m lmax-v1.0 2 M B6D2F1/J wgEncodeUwDnase416bC57bl6MAdult8wksPkRep2 Peaks Immortal cells myeloid progenitor cells, CD34+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Regions of enriched signal in experiment 416B DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase416bC57bl6MAdult8wksPkRep1 416B P 1 immortalized 416B DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-22 wgEncodeEM001717 1717 GSM1014163 Stam UW-m lmax-v1.0 1 M B6D2F1/J wgEncodeUwDnase416bC57bl6MAdult8wksPkRep1 Peaks Immortal cells myeloid progenitor cells, CD34+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Regions of enriched signal in experiment 416B DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase3134RiiiMImmortalPkRep2 3134 P 2 immortalized 3134 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-10 2012-02-10 wgEncodeEM001721 1721 GSM1014196 Stam UW-m lmax-v1.1 2 M RIII wgEncodeUwDnase3134RiiiMImmortalPkRep2 Peaks Immortal cells Mammary DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male High mammary tumor incidence in unfostered substrains. Regions of enriched signal in experiment 3134 DNaseI HS Peaks Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase3134RiiiMImmortalPkRep1 3134 P 1 immortalized 3134 DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001721 1721 GSM1014196 Stam UW-m lmax-v1.0 1 M RIII wgEncodeUwDnase3134RiiiMImmortalPkRep1 Peaks Immortal cells Mammary DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male High mammary tumor incidence in unfostered substrains. Regions of enriched signal in experiment 3134 DNaseI HS Peaks Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseViewHotspots Hot Spots DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0HotspotsRep2 ZhBTc4 H 2 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001735 1735 GSM1014169 Stam UW-m Hotspot-v5.1 2 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0HotspotsRep2 None Hotspots Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. ChIP-seq affinity zones identified using the HotSpot algorithm ZhBTc4 DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0HotspotsRep1V2 ZhBTc4 H 1 E0 ZhBTc4 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2011-05-06 2012-02-06 wgEncodeEM001735 1735 GSM1014169 Stam UW-m DS17616 Hotspot-v5.2 1 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0HotspotsRep1V2 None Hotspots Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. ChIP-seq affinity zones identified using the HotSpot algorithm ZhBTc4 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0Diffb6hHotspotsRep2 ZhBTc4 dPB 6 H 2 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003407 3407 GSM1014150 Stam UW-m DS15860 Hotspot-v5.2 2 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0Diffb6hHotspotsRep2 None diffProtB_6hr Hotspots Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 6 hours. Doxycycline added to a final concentration of 100 ng/ml. (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm ZhBTc4 diffProtB 6 hr DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0Diffb6hHotspotsRep1 ZhBTc4 dPB 6 H 1 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003407 3407 GSM1014150 Stam UW-m DS15236 Hotspot-v5.2 1 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0Diffb6hHotspotsRep1 None diffProtB_6hr Hotspots Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 6 hours. Doxycycline added to a final concentration of 100 ng/ml. (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm ZhBTc4 diffProtB 6 hr DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0Diffb24hHotspotsRep2 ZhBTc4 dPB 24 H 2 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003406 3406 GSM1014152 Stam UW-m DS15299 Hotspot-v5.2 2 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0Diffb24hHotspotsRep2 None diffProtB_24hr Hotspots Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 24 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm ZhBTc4 diffProtB 24 hr DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseZhbtc4129olaME0Diffb24hHotspotsRep1 ZhBTc4 dPB 24 H 1 E0 ZhBTc4 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003406 3406 GSM1014152 Stam UW-m DS17562 Hotspot-v5.2 1 M 129/Ola wgEncodeUwDnaseZhbtc4129olaME0Diffb24hHotspotsRep1 None diffProtB_24hr Hotspots Embryonic day 0 (stem cell) Undifferentiated mouse embryonic stem cells DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. Oct4 repression with Doxycycline in ZhBTc4 ES cell culture harvested at 24 hours. Doxycycline added to a final concentration of 100 ng/ml (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm ZhBTc4 diffProtB 24 hr DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6ME18halfHotspotsRep2 Brain E18.5 H 2 E18.5 WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM003396 3396 GSM1014184 Stam UW-m DS15269 Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6ME18halfHotspotsRep2 Pooled Hotspots Embryonic day 18.5 Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Whole Brain Embryonic Day 18.5 DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6ME18halfHotspotsRep1 Brain E18.5 H 1 E18.5 WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2011-12-15 2012-09-15 wgEncodeEM003396 3396 GSM1014184 Stam UW-m DS19690 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6ME18halfHotspotsRep1 Pooled Hotspots Embryonic day 18.5 Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Whole Brain Embryonic Day 18.5 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6ME14halfHotspotsRep2 Brain E14.5 H 2 E14.5 WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2010-07-27 2011-04-26 wgEncodeEM001726 1726 GSM1014197 Stam UW-m Hotspot-v5.1 2 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6ME14halfHotspotsRep2 Individual Hotspots Embryonic day 14.5 Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual ChIP-seq affinity zones identified using the HotSpot algorithm Whole Brain Embryonic Day 14.5 DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6ME14halfHotspotsRep1 Brain E14.5 H 1 E14.5 WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001726 1726 GSM1014197 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6ME14halfHotspotsRep1 Individual Hotspots Embryonic day 14.5 Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual ChIP-seq affinity zones identified using the HotSpot algorithm Whole Brain Embryonic Day 14.5 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6MAdult8wksHotspotsRep2 Brain A8w H 2 adult-8wks WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001729 1729 GSM1014151 Stam UW-m Hotspot-v5.1 2 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6MAdult8wksHotspotsRep2 Individual Hotspots Adult 8 weeks Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual ChIP-seq affinity zones identified using the HotSpot algorithm Whole Brain Adult 8 Weeks DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseWbrainC57bl6MAdult8wksHotspotsRep1 Brain A8w H 1 adult-8wks WholeBrain DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001729 1729 GSM1014151 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseWbrainC57bl6MAdult8wksHotspotsRep1 Individual Hotspots Adult 8 weeks Whole Brain DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual ChIP-seq affinity zones identified using the HotSpot algorithm Whole Brain Adult 8 Weeks DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTregaC57bl6MAdult8wksHotspotsRep2 TReg-Act H 2 adult-8wks TReg-Activated DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003404 3404 GSM1014200 Stam UW-m DS17077 Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseTregaC57bl6MAdult8wksHotspotsRep2 None Hotspots Adult 8 weeks Activated primary T regulatory cells, isolated ex vivo DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse ChIP-seq affinity zones identified using the HotSpot algorithm TReg-Activated DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTregaC57bl6MAdult8wksHotspotsRep1 TReg-Act H 1 adult-8wks TReg-Activated DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003404 3404 GSM1014200 Stam UW-m DS20149 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseTregaC57bl6MAdult8wksHotspotsRep1 None Hotspots Adult 8 weeks Activated primary T regulatory cells, isolated ex vivo DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse ChIP-seq affinity zones identified using the HotSpot algorithm TReg-Activated DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTregC57bl6MAdult8wksHotspotsRep2 TReg H 2 adult-8wks TReg DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001732 1732 GSM1014148 Stam UW-m Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseTregC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Regulatory T cells CD4+,CD25+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm TReg DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTregC57bl6MAdult8wksHotspotsRep1 TReg H 1 adult-8wks TReg DnaseSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001732 1732 GSM1014148 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseTregC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Regulatory T cells CD4+,CD25+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm TReg DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseThymusC57bl6MAdult8wksHotspotsRep2 Thymus H 2 adult-8wks Thymus DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM003395 3395 GSM1014185 Stam UW-m DS18890 Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseThymusC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Thymus DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Thymus DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseThymusC57bl6MAdult8wksHotspotsRep1 Thymus H 1 adult-8wks Thymus DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM003395 3395 GSM1014185 Stam UW-m DS18819 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseThymusC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Thymus DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Thymus DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseThelpaC57bl6MAdult8wksHotspotsRep2 THelper-Act H 2 adult-8wks THelper-Activated DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003403 3403 GSM1014149 Stam UW-m DS18848 Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseThelpaC57bl6MAdult8wksHotspotsRep2 None Hotspots Adult 8 weeks Activated primary CD4 effector cells, isolated ex vivo DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse ChIP-seq affinity zones identified using the HotSpot algorithm THelper-Activated DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseThelpaC57bl6MAdult8wksHotspotsRep1 THelper-Act H 1 adult-8wks THelper-Activated DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003403 3403 GSM1014149 Stam UW-m DS17070 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseThelpaC57bl6MAdult8wksHotspotsRep1 None Hotspots Adult 8 weeks Activated primary CD4 effector cells, isolated ex vivo DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse ChIP-seq affinity zones identified using the HotSpot algorithm THelper-Activated DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTnaiveC57bl6MAdult8wksHotspotsRep2 T-Naive H 2 adult-8wks T-Naive DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001725 1725 GSM1014192 Stam UW-m Hotspot-v5.1 2 M C57BL/6 wgEncodeUwDnaseTnaiveC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Naive T cells: CD4+, CD25- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm T-Naive DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseTnaiveC57bl6MAdult8wksHotspotsRep1 T-Naive H 1 adult-8wks T-Naive DnaseSeq ENCODE Mar 2012 Freeze 2011-04-18 2012-01-18 wgEncodeEM001725 1725 GSM1014192 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseTnaiveC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Naive T cells: CD4+, CD25- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm T-Naive DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseSpleenC57bl6MAdult8wksHotspotsRep2 Spleen H 2 adult-8wks Spleen DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM003394 3394 GSM1014182 Stam UW-m DS18884 Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseSpleenC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Spleen DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Spleen DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseSpleenC57bl6MAdult8wksHotspotsRep1 Spleen H 1 adult-8wks Spleen DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM003394 3394 GSM1014182 Stam UW-m DS18870 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseSpleenC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Spleen DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Spleen DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksHotspotsRep2 Sk Muscle H 2 adult-8wks SkMuscle DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-19 2012-09-19 wgEncodeEM003399 3399 GSM1014189 Stam UW-m DS18892 Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Skeletal Muscle DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Skeletal Muscle DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksHotspotsRep1 Sk Muscle H 1 adult-8wks SkMuscle DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-19 2012-09-19 wgEncodeEM003399 3399 GSM1014189 Stam UW-m DS18130 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Skeletal Muscle DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Skeletal Muscle DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseRetinaC57bl6MNew1daysHotspotsRep1 Retina N1d H 1 newborn-1days Retina DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-20 2012-09-20 wgEncodeEM003400 3400 GSM1014188 Stam UW-m DS20004 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseRetinaC57bl6MNew1daysHotspotsRep1 Pooled Hotspots Newborn 1 day Retina DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Retina Newborn 1 Day DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseRetinaC57bl6MAdult8wksHotspotsRep1 Retina A8w H 1 adult-8wks Retina DnaseSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM003402 3402 GSM1014175 Stam UW-m DS19060 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseRetinaC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Retina DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Retina Adult 8 Weeks DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseRetinaC57bl6MAdult1wksHotspotsRep1 Retina A1w H 1 adult-1wks Retina DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-19 2012-09-19 wgEncodeEM003398 3398 GSM1014198 Stam UW-m DS20000 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseRetinaC57bl6MAdult1wksHotspotsRep1 Pooled Hotspots Adult 1 week Retina DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Retina Adult 1 week DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnasePatskiSpbl6MImmortalHotspotsRep2 Patski H 2 immortalized Patski DnaseSeq ENCODE Mar 2012 Freeze 2011-05-10 2012-02-10 wgEncodeEM001736 1736 GSM1014171 Stam UW-m Hotspot-v5.1 2 M Spretus.BL6-Xist wgEncodeUwDnasePatskiSpbl6MImmortalHotspotsRep2 None Hotspots Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. ChIP-seq affinity zones identified using the HotSpot algorithm Patski DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnasePatskiSpbl6MImmortalHotspotsRep1 Patski H 1 immortalized Patski DnaseSeq ENCODE Mar 2012 Freeze 2011-05-10 2012-02-10 wgEncodeEM001736 1736 GSM1014171 Stam UW-m Hotspot-v5.1 1 M Spretus.BL6-Xist wgEncodeUwDnasePatskiSpbl6MImmortalHotspotsRep1 None Hotspots Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. ChIP-seq affinity zones identified using the HotSpot algorithm Patski DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseNih3t3NihsMImmortalHotspotsRep2 NIH-3T3 H 2 immortalized NIH-3T3 DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001936 1936 GSM1014177 Stam UW-m Hotspot-v5.1 2 M NIH/Swiss wgEncodeUwDnaseNih3t3NihsMImmortalHotspotsRep2 None Hotspots Immortal cells fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. ChIP-seq affinity zones identified using the HotSpot algorithm NIH-3T3 DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseNih3t3NihsMImmortalHotspotsRep1 NIH-3T3 H 1 immortalized NIH-3T3 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-21 2011-12-15 2012-09-15 wgEncodeEM001936 1936 GSM1014177 Stam UW-m DS16900 Hotspot-v5.2 1 M NIH/Swiss wgEncodeUwDnaseNih3t3NihsMImmortalHotspotsRep1 Pooled Hotspots Immortal cells fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm NIH-3T3 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalHotspotsRep2 mG/ER H 2 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003405 3405 GSM1014176 Stam UW-m DS15395 Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalHotspotsRep2 None Hotspots Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse ChIP-seq affinity zones identified using the HotSpot algorithm mG/ER DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalHotspotsRep1 mG/ER H 1 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003405 3405 GSM1014176 Stam UW-m DS15400 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalHotspotsRep1 None Hotspots Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse ChIP-seq affinity zones identified using the HotSpot algorithm mG/ER DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalDiffc48hHotspotsRep2 mG/ER dPC 48 H 2 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003409 3409 GSM1014180 Stam UW-m DS15415 Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalDiffc48hHotspotsRep2 None diffProtC_48hr Hotspots Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse 48 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm mG/ER diffProtC 48 hr DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalDiffc48hHotspotsRep1 mG/ER dPC 48 H 1 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003409 3409 GSM1014180 Stam UW-m DS15420 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalDiffc48hHotspotsRep1 None diffProtC_48hr Hotspots Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse 48 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm mG/ER diffProtC 48 hr DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalDiffc24hHotspotsRep2 mG/ER dPC 24 H 2 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003408 3408 GSM1014181 Stam UW-m DS15405 Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalDiffc24hHotspotsRep2 None diffProtC_24hr Hotspots Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse 24 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm mG/ER diffProtC 24 hr DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMgerUknImmortalDiffc24hHotspotsRep1 mG/ER dPC 24 H 1 adult-8wks mG/ER DnaseSeq ENCODE Mar 2012 Freeze 2012-02-29 2012-11-29 wgEncodeEM003408 3408 GSM1014181 Stam UW-m DS15410 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseMgerUknImmortalDiffc24hHotspotsRep1 None diffProtC_24hr Hotspots Adult 8 weeks MEL-GATA-1-ER, This is a mouse suspension cell line derived from MEL cells by stable transfection with a GATA-1-ER fusion protein construct as described by Choe et al., 2003 (Cancer Res 63, 6363-6369, 2003). These cells can be terminally differentiated into mature erythroid cells with &Beta;-estradiol treatment DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse 24 hour differentiation time point of mG/ER cells towards red blood cells after treatment with estradiol. Estradiol 10^-7 M final concentration (Stam) ChIP-seq affinity zones identified using the HotSpot algorithm mG/ER diffProtC 24 hr DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMesodermCd1ME11halfHotspotsRep2 Mesoderm H 2 E11.5 Mesoderm DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001935 1935 GSM1014178 Stam UW-m Hotspot-v5.2 2 M CD-1 wgEncodeUwDnaseMesodermCd1ME11halfHotspotsRep2 Pooled Hotspots Embryonic day 11.5 axial somatic and lateral plate mesoderm from eviscerated headless, limbless embryos DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Mesoderm DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMesodermCd1ME11halfHotspotsRep1 Mesoderm H 1 E11.5 Mesoderm DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001935 1935 GSM1014178 Stam UW-m Hotspot-v5.2 1 M CD-1 wgEncodeUwDnaseMesodermCd1ME11halfHotspotsRep1 Pooled Hotspots Embryonic day 11.5 axial somatic and lateral plate mesoderm from eviscerated headless, limbless embryos DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Mesoderm DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMelC57bl6MAdult8wksHotspotsRep2 MEL H 2 immortalized MEL DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001724 1724 GSM1014191 Stam UW-m Hotspot-v5.1 2 M Unknown wgEncodeUwDnaseMelC57bl6MAdult8wksHotspotsRep2 Hotspots Immortal cells Leukemia (K562 analog) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin ChIP-seq affinity zones identified using the HotSpot algorithm MEL DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseMelC57bl6MAdult8wksHotspotsRep1 MEL H 1 immortalized MEL DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001724 1724 GSM1014191 Stam UW-m Hotspot-v5.1 1 M Unknown wgEncodeUwDnaseMelC57bl6MAdult8wksHotspotsRep1 Hotspots Immortal cells Leukemia (K562 analog) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin ChIP-seq affinity zones identified using the HotSpot algorithm MEL DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLungC57bl6MAdult8wksHotspotsRep2 Lung H 2 adult-8wks Lung DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001723 1723 GSM1014194 Stam UW-m Hotspot-v5.1 2 M C57BL/6 wgEncodeUwDnaseLungC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Lung DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Lung DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLungC57bl6MAdult8wksHotspotsRep1 Lung H 1 adult-8wks Lung DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001723 1723 GSM1014194 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseLungC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Lung DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Lung DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiver129dlcrME14halfHotspotsRep2 Livr 1D E14.5 H 2 E14.5 Liver DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003418 3418 GSM1014161 Stam UW-m DS19531 Hotspot-v5.2 2 M 129.DLCR/DLCR wgEncodeUwDnaseLiver129dlcrME14halfHotspotsRep2 Pooled Hotspots Embryonic day 14.5 Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male 129 strain mouse with homozygous deletion of the beta-globin LCR region, see Bender et. al. (2000). Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region. Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiver129dlcrME14halfHotspotsRep1 Livr 1D E14.5 H 1 E14.5 Liver DnaseSeq ENCODE Jul 2012 Freeze 2012-08-20 2013-05-20 wgEncodeEM003418 3418 GSM1014161 Stam UW-m DS19241 Hotspot-v5.2 1 M 129.DLCR/DLCR wgEncodeUwDnaseLiver129dlcrME14halfHotspotsRep1 Pooled Hotspots Embryonic day 14.5 Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male 129 strain mouse with homozygous deletion of the beta-globin LCR region, see Bender et. al. (2000). Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region. Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiverS129ME14halfHotspotsRep1 Livr 1 E14.5 H 1 E14.5 Liver DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003419 3419 GSM1014162 Stam UW-m DS19246 Hotspot-v5.2 1 M 129 wgEncodeUwDnaseLiverS129ME14halfHotspotsRep1 Pooled Hotspots Embryonic day 14.5 Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Strain 129, has widely available embryonic stem cells Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Liver 129 Embryonic Day 14.5 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiverC57bl6ME14halfHotspotsRep1 Livr C E14.5 H 1 E14.5 Liver DnaseSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM003401 3401 GSM1014183 Stam UW-m DS20666 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseLiverC57bl6ME14halfHotspotsRep1 Pooled Hotspots Embryonic day 14.5 Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Liver C57BL/6 Embryonic Day 14.5 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep2 Livr C A8w H 2 adult-8wks Liver DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001720 1720 GSM1014195 Stam UW-m Hotspot-v5.1 2 M C57BL/6 wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Liver C57BL/6 Adult 8 Weeks DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep1 Livr C A8w H 1 adult-8wks Liver DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-23 wgEncodeEM001720 1720 GSM1014195 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Liver DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Liver C57BL/6 Adult 8 Weeks DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLgintC57bl6MAdult8wksHotspotsRep2 Lg Intestine H 2 adult-8wks LgIntestine DnaseSeq ENCODE Mar 2012 Freeze 2012-02-15 2012-11-15 wgEncodeEM003397 3397 GSM1014186 Stam UW-m DS18784 Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseLgintC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Large Intestine DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Large Intestine DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseLgintC57bl6MAdult8wksHotspotsRep1 Lg Intestine H 1 adult-8wks LgIntestine DnaseSeq ENCODE Mar 2012 Freeze 2011-12-19 2012-09-19 wgEncodeEM003397 3397 GSM1014186 Stam UW-m DS19140 Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseLgintC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Large Intestine DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Large Intestine DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseKidneyC57bl6MAdult8wksHotspotsRep2 Kidney H 2 adult-8wks Kidney DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001722 1722 GSM1014193 Stam UW-m Hotspot-v5.1 2 M C57BL/6 wgEncodeUwDnaseKidneyC57bl6MAdult8wksHotspotsRep2 Individual Hotspots Adult 8 weeks Kidney DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual ChIP-seq affinity zones identified using the HotSpot algorithm Kidney DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseKidneyC57bl6MAdult8wksHotspotsRep1 Kidney H 1 adult-8wks Kidney DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001722 1722 GSM1014193 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseKidneyC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Kidney DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Kidney DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHlbudCd1ME11halfHotspotsRep2 Hind Limb Bud H 2 E11.5 HindlimbBud DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001934 1934 GSM1014179 Stam UW-m Hotspot-v5.2 2 M CD-1 wgEncodeUwDnaseHlbudCd1ME11halfHotspotsRep2 Pooled Hotspots Embryonic day 11.5 embryo hindlimb buds DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Hind Limb Bud DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHlbudCd1ME11halfHotspotsRep1 Hind Limb Bud H 1 E11.5 HindlimbBud DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001934 1934 GSM1014179 Stam UW-m Hotspot-v5.2 1 M CD-1 wgEncodeUwDnaseHlbudCd1ME11halfHotspotsRep1 Pooled Hotspots Embryonic day 11.5 embryo hindlimb buds DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Hind Limb Bud DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHeartC57bl6MAdult8wksHotspotsRep2 Heart H 2 adult-8wks Heart DnaseSeq ENCODE Mar 2012 Freeze 2011-12-15 2012-09-15 wgEncodeEM001730 1730 GSM1014166 Stam UW-m DS18138 Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseHeartC57bl6MAdult8wksHotspotsRep2 Individual Hotspots Adult 8 weeks Heart DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual ChIP-seq affinity zones identified using the HotSpot algorithm Heart DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHeartC57bl6MAdult8wksHotspotsRep1 Heart H 1 adult-8wks Heart DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001730 1730 GSM1014166 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseHeartC57bl6MAdult8wksHotspotsRep1 Individual Hotspots Adult 8 weeks Heart DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual ChIP-seq affinity zones identified using the HotSpot algorithm Heart DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHlembryoCd1ME11halfHotspotsRep2 Headless Emb H 2 E11.5 HeadlessEmbryo DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001933 1933 GSM1014172 Stam UW-m Hotspot-v5.2 2 M CD-1 wgEncodeUwDnaseHlembryoCd1ME11halfHotspotsRep2 Pooled Hotspots Embryonic day 11.5 Whole embryos with heads removed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Headless Embryo DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseHlembryoCd1ME11halfHotspotsRep1 Headless Emb H 1 E11.5 HeadlessEmbryo DnaseSeq ENCODE Mar 2012 Freeze 2011-12-14 2012-09-14 wgEncodeEM001933 1933 GSM1014172 Stam UW-m DS17129 Hotspot-v5.2 1 M CD-1 wgEncodeUwDnaseHlembryoCd1ME11halfHotspotsRep1 Pooled Hotspots Embryonic day 11.5 Whole embryos with heads removed DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Headless Embryo DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseGfatC57bl6MAdult8wksHotspotsRep2 Gen Fat Pad H 2 adult-8wks GenitalFatPad DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001932 1932 GSM1014173 Stam UW-m Hotspot-v5.2 2 M C57BL/6 wgEncodeUwDnaseGfatC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Genital Adipose tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Genital Fat Pad DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseGfatC57bl6MAdult8wksHotspotsRep1 Gen Fat Pad H 1 adult-8wks GenitalFatPad DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001932 1932 GSM1014173 Stam UW-m Hotspot-v5.2 1 M C57BL/6 wgEncodeUwDnaseGfatC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Genital Adipose tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Genital Fat Pad DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFlbudCd1ME11halfHotspotsRep2 Fore Limb Bud H 2 E11.5 ForelimbBud DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001931 1931 GSM1014174 Stam UW-m Hotspot-v5.2 2 M CD-1 wgEncodeUwDnaseFlbudCd1ME11halfHotspotsRep2 Pooled Hotspots Embryonic day 11.5 embryo forelimb buds DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Fore Limb Bud DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFlbudCd1ME11halfHotspotsRep1 Fore Limb Bud H 1 E11.5 ForelimbBud DnaseSeq ENCODE Mar 2012 Freeze 2011-06-29 2012-03-29 wgEncodeEM001931 1931 GSM1014174 Stam UW-m Hotspot-v5.2 1 M CD-1 wgEncodeUwDnaseFlbudCd1ME11halfHotspotsRep1 Pooled Hotspots Embryonic day 11.5 embryo forelimb buds DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Fore Limb Bud DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFibroblastC57bl6MAdult8wksHotspotsRep2 Fibroblast H 2 adult-8wks Fibroblast DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-23 wgEncodeEM001719 1719 GSM1014199 Stam UW-m Hotspot-v5.1 2 M C57BL/6 wgEncodeUwDnaseFibroblastC57bl6MAdult8wksHotspotsRep2 Hotspots Adult 8 weeks Fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse ChIP-seq affinity zones identified using the HotSpot algorithm Fibroblast DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFibroblastC57bl6MAdult8wksHotspotsRep1 Fibroblast H 1 adult-8wks Fibroblast DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-23 wgEncodeEM001719 1719 GSM1014199 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseFibroblastC57bl6MAdult8wksHotspotsRep1 Hotspots Adult 8 weeks Fibroblast DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse ChIP-seq affinity zones identified using the HotSpot algorithm Fibroblast DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFatC57bl6MAdult8wksHotspotsRep2 Fat Pad H 2 adult-8wks FatPad DnaseSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001731 1731 GSM1014165 Stam UW-m Hotspot-v5.1 2 M C57BL/6 wgEncodeUwDnaseFatC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Adipose tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Fat Pad DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseFatC57bl6MAdult8wksHotspotsRep1 Fat Pad H 1 adult-8wks FatPad DnaseSeq ENCODE Mar 2012 Freeze 2011-05-02 2012-02-02 wgEncodeEM001731 1731 GSM1014165 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseFatC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Adipose tissue DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Fat Pad DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEsww6koUknME0HotspotsRep2 ES-WW6 F1KO H 2 E0 ES-WW6_F1KO DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEM003411 3411 GSM1014160 Stam UW-m DS18365 Hotspot-v5.2 2 M Unknown wgEncodeUwDnaseEsww6koUknME0HotspotsRep2 None Hotspots Embryonic day 0 (stem cell) Histone H1c, H1d, H1e triple null mouse embryonic stem cell line derived from ES-WW6 cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin ChIP-seq affinity zones identified using the HotSpot algorithm ES-WW6 F1KO DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEsww6koUknME0HotspotsRep1 ES-WW6 F1KO H 1 E0 ES-WW6_F1KO DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEM003411 3411 GSM1014160 Stam UW-m DS17063 Hotspot-v5.2 1 M Unknown wgEncodeUwDnaseEsww6koUknME0HotspotsRep1 None Hotspots Embryonic day 0 (stem cell) Histone H1c, H1d, H1e triple null mouse embryonic stem cell line derived from ES-WW6 cells. DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin ChIP-seq affinity zones identified using the HotSpot algorithm ES-WW6 F1KO DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEsww6UknME0HotspotsRep2 ES-WW6 H 2 E0 ES-WW6 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEM003410 3410 GSM1014159 Stam UW-m DS17613 Hotspot-v5.2 2 M Unknown wgEncodeUwDnaseEsww6UknME0HotspotsRep2 None Hotspots Embryonic day 0 (stem cell) ES-cells isolated from mix of ~20% C57/B6J, ~75% 129/Sv and ~5% SJL strains DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin ChIP-seq affinity zones identified using the HotSpot algorithm ES-WW6 DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEsww6UknME0HotspotsRep1 ES-WW6 H 1 E0 ES-WW6 DnaseSeq ENCODE Jul 2012 Freeze 2012-07-18 2013-04-17 wgEncodeEM003410 3410 GSM1014159 Stam UW-m DS17060 Hotspot-v5.2 1 M Unknown wgEncodeUwDnaseEsww6UknME0HotspotsRep1 None Hotspots Embryonic day 0 (stem cell) ES-cells isolated from mix of ~20% C57/B6J, ~75% 129/Sv and ~5% SJL strains DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Unknown strain origin ChIP-seq affinity zones identified using the HotSpot algorithm ES-WW6 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEse14129olaME0HotspotsRep2 ES-E14 H 2 E0 ES-E14 DnaseSeq ENCODE Mar 2012 Freeze 2012-02-27 2012-11-27 wgEncodeEM003417 3417 GSM1014154 Stam UW-m DS18505 Hotspot-v5.2 2 M 129/Ola wgEncodeUwDnaseEse14129olaME0HotspotsRep2 None Hotspots Embryonic day 0 (stem cell) mouse embryonic stem cell line E14 DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. ChIP-seq affinity zones identified using the HotSpot algorithm ES-E14 DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEse14129olaME0HotspotsRep1 ES-E14 H 1 E0 ES-E14 DnaseSeq ENCODE Jul 2012 Freeze 2012-05-01 2013-02-01 wgEncodeEM003417 3417 GSM1014154 Stam UW-m DS21450 Hotspot-v5.2 1 M 129/Ola wgEncodeUwDnaseEse14129olaME0HotspotsRep1 None Hotspots Embryonic day 0 (stem cell) mouse embryonic stem cell line E14 DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice. ChIP-seq affinity zones identified using the HotSpot algorithm ES-E14 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEscj7S129ME0HotspotsRep2 ES-CJ7 H 2 E0 ES-CJ7 DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001728 1728 GSM1014187 Stam UW-m Hotspot-v5.1 2 M 129S1/SVImJ wgEncodeUwDnaseEscj7S129ME0HotspotsRep2 Hotspots Embryonic day 0 (stem cell) ES-cells were originally isolated from 129S1/SVImJ mice by Swiatek PJ et al. in 1993 ("Perinatal lethality and defects in hindbrain development in mice homozygous for a targeted mutation of the zinc finger gene Krox20". Swiatek PJ, Gridley T. Genes Dev. 1993 Nov,7(11):2071-84.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Control inbred strain of the steel-derived ES cells. ChIP-seq affinity zones identified using the HotSpot algorithm ES-CJ7 DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEscj7S129ME0HotspotsRep1 ES-CJ7 H 1 E0 ES-CJ7 DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001728 1728 GSM1014187 Stam UW-m Hotspot-v5.1 1 M 129S1/SVImJ wgEncodeUwDnaseEscj7S129ME0HotspotsRep1 Hotspots Embryonic day 0 (stem cell) ES-cells were originally isolated from 129S1/SVImJ mice by Swiatek PJ et al. in 1993 ("Perinatal lethality and defects in hindbrain development in mice homozygous for a targeted mutation of the zinc finger gene Krox20". Swiatek PJ, Gridley T. Genes Dev. 1993 Nov,7(11):2071-84.) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Control inbred strain of the steel-derived ES cells. ChIP-seq affinity zones identified using the HotSpot algorithm ES-CJ7 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEpcpppCd1ME14halfHotspotsRep1 EPC +++ H 1 E14.5 EPC_(CD117+_CD71+_TER119+) DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003412 3412 GSM1014157 Stam UW-m DS20999 Hotspot-v5.2 1 M CD-1 wgEncodeUwDnaseEpcpppCd1ME14halfHotspotsRep1 None Hotspots Embryonic day 14.5 liver fraction CD117+,CD71+,TER119+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. ChIP-seq affinity zones identified using the HotSpot algorithm EPC (CD117+,CD71+,TER119+) DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEpcppmCd1ME14halfHotspotsRep1 EPC ++- H 1 E14.5 EPC_(CD117+_CD71+_TER119-) DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003413 3413 GSM1014158 Stam UW-m DS20994 Hotspot-v5.2 1 M CD-1 wgEncodeUwDnaseEpcppmCd1ME14halfHotspotsRep1 None Hotspots Embryonic day 14.5 liver fraction CD117+,CD71+,TER119- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. ChIP-seq affinity zones identified using the HotSpot algorithm EPC (CD117+,CD71+,TER119-) DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEpcpmmCd1ME14halfHotspotsRep1 EPC +-- H 1 E14.5 EPC_(CD117+_CD71-_TER119-) DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003414 3414 GSM1014155 Stam UW-m DS20991 Hotspot-v5.2 1 M CD-1 wgEncodeUwDnaseEpcpmmCd1ME14halfHotspotsRep1 None Hotspots Embryonic day 14.5 liver fraction CD117+,CD71-,TER119- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. ChIP-seq affinity zones identified using the HotSpot algorithm EPC (CD117+,CD71-,TER119-) DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseEpcmppCd1ME14halfHotspotsRep1 EPC -++ H 1 E14.5 EPC_(CD117-_CD71+_TER119+) DnaseSeq ENCODE Jul 2012 Freeze 2012-07-25 2013-04-25 wgEncodeEM003415 3415 GSM1014156 Stam UW-m DS20937 Hotspot-v5.2 1 M CD-1 wgEncodeUwDnaseEpcmppCd1ME14halfHotspotsRep1 None Hotspots Embryonic day 14.5 liver fraction CD117-,CD71+,TER119+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. ChIP-seq affinity zones identified using the HotSpot algorithm EPC (CD117-,CD71+,TER119+) DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCh122a4bFImmortalHotspotsRep2 CH12 H 2 immortalized CH12 DnaseSeq ENCODE Jul 2012 Freeze 2012-08-16 2013-05-16 wgEncodeEM003416 3416 GSM1014153 Stam UW-m DS22536 Hotspot-v5.2 2 F B10.H-2aH-4bp/Wts wgEncodeUwDnaseCh122a4bFImmortalHotspotsRep2 None Hotspots Immortal cells B-cell lymphoma (GM12878 analog) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 ChIP-seq affinity zones identified using the HotSpot algorithm CH12 DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCh122a4bFImmortalHotspotsRep1 CH12 H 1 immortalized CH12 DnaseSeq ENCODE Jul 2012 Freeze 2012-08-16 2013-05-16 wgEncodeEM003416 3416 GSM1014153 Stam UW-m DS22542 Hotspot-v5.2 1 F B10.H-2aH-4bp/Wts wgEncodeUwDnaseCh122a4bFImmortalHotspotsRep1 None Hotspots Immortal cells B-cell lymphoma (GM12878 analog) DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Female Derived by inbreeding from selected F2 progeny of B10.A X B10.129 ChIP-seq affinity zones identified using the HotSpot algorithm CH12 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCerebrumC57bl6MAdult8wksHotspotsRep2 Cerebrum H 2 adult-8wks Cerebrum DnaseSeq ENCODE Mar 2012 Freeze 2010-07-22 2011-04-22 wgEncodeEM001718 1718 GSM1014168 Stam UW-m Hotspot-v5.1 2 M C57BL/6 wgEncodeUwDnaseCerebrumC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Cerebrum DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Cerebrum DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCerebrumC57bl6MAdult8wksHotspotsRep1 Cerebrum H 1 adult-8wks Cerebrum DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-22 wgEncodeEM001718 1718 GSM1014168 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseCerebrumC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Cerebrum DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Cerebrum DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCbellumC57bl6MAdult8wksHotspotsRep2 Cerebellum H 2 adult-8wks Cerebellum DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001716 1716 GSM1014164 Stam UW-m Hotspot-v5.1 2 M C57BL/6 wgEncodeUwDnaseCbellumC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks Cerebellum DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Cerebellum DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseCerebellumC57bl6MAdult8wksHotspotsRep1 Cerebellum H 1 adult-8wks Cerebellum DnaseSeq ENCODE Mar 2012 Freeze 2010-07-21 2011-04-20 wgEncodeEM001716 1716 GSM1014164 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseCerebellumC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks Cerebellum DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm Cerebellum DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksHotspotsRep2 Bcell (CD43-) H 2 adult-8wks B-cell_(CD43-) DnaseSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001734 1734 GSM1014170 Stam UW-m Hotspot-v5.1 2 M C57BL/6 wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksHotspotsRep2 Pooled Hotspots Adult 8 weeks mouse spleen B cells, CD43-,CD11b- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm B-cell (CD43-) DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksHotspotsRep1 Bcell (CD43-) H 1 adult-8wks B-cell_(CD43-) DnaseSeq ENCODE Mar 2012 Freeze 2011-05-06 2012-02-06 wgEncodeEM001734 1734 GSM1014170 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks mouse spleen B cells, CD43-,CD11b- DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm B-cell (CD43-) DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksHotspotsRep2 Bcell (CD19+) H 2 adult-8wks B-cell_(CD19+) DnaseSeq ENCODE Mar 2012 Freeze 2010-07-28 2011-04-28 wgEncodeEM001727 1727 GSM1014190 Stam UW-m Hotspot-v5.1 2 M C57BL/6 wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksHotspotsRep2 Hotspots Adult 8 weeks B Cell , CD19+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse ChIP-seq affinity zones identified using the HotSpot algorithm B-cell (CD19+) DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksHotspotsRep1 Bcell (CD19+) H 1 adult-8wks B-cell_(CD19+) DnaseSeq ENCODE Mar 2012 Freeze 2011-04-19 2012-01-19 wgEncodeEM001727 1727 GSM1014190 Stam UW-m Hotspot-v5.1 1 M C57BL/6 wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksHotspotsRep1 Pooled Hotspots Adult 8 weeks B Cell , CD19+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms ChIP-seq affinity zones identified using the HotSpot algorithm B-cell (CD19+) DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseA20BalbcannMAdult8wksHotspotsRep2 A20 H 2 immortalized A20 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-03 2012-02-03 wgEncodeEM001733 1733 GSM1014167 Stam UW-m Hotspot-v5.1 2 M BALB/cAnN wgEncodeUwDnaseA20BalbcannMAdult8wksHotspotsRep2 None Hotspots Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male ccMyeloma high incidence H2d ChIP-seq affinity zones identified using the HotSpot algorithm A20 DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnaseA20BalbcannMAdult8wksHotspotsRep1 A20 H 1 immortalized A20 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-03 2012-02-03 wgEncodeEM001733 1733 GSM1014167 Stam UW-m Hotspot-v5.1 1 M BALB/cAnN wgEncodeUwDnaseA20BalbcannMAdult8wksHotspotsRep1 None Hotspots Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male ccMyeloma high incidence H2d ChIP-seq affinity zones identified using the HotSpot algorithm A20 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase416bC57bl6MAdult8wksHotspotsRep2 416B H 2 immortalized 416B DnaseSeq ENCODE Mar 2012 Freeze 2010-07-22 2011-04-22 wgEncodeEM001717 1717 GSM1014163 Stam UW-m Hotspot-v5.1 2 M B6D2F1/J wgEncodeUwDnase416bC57bl6MAdult8wksHotspotsRep2 Hotspots Immortal cells myeloid progenitor cells, CD34+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. ChIP-seq affinity zones identified using the HotSpot algorithm 416B DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase416bC57bl6MAdult8wksHotspotsRep1 416B H 1 immortalized 416B DnaseSeq ENCODE Mar 2012 Freeze 2010-07-23 2011-04-22 wgEncodeEM001717 1717 GSM1014163 Stam UW-m Hotspot-v5.1 1 M B6D2F1/J wgEncodeUwDnase416bC57bl6MAdult8wksHotspotsRep1 Hotspots Immortal cells myeloid progenitor cells, CD34+ DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. ChIP-seq affinity zones identified using the HotSpot algorithm 416B DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase3134RiiiMImmortalHotspotsRep2 3134 H 2 immortalized 3134 DnaseSeq ENCODE Mar 2012 Freeze 2011-05-10 2012-02-10 wgEncodeEM001721 1721 GSM1014196 Stam UW-m Hotspot-v5.1 2 M RIII wgEncodeUwDnase3134RiiiMImmortalHotspotsRep2 Hotspots Immortal cells Mammary DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male High mammary tumor incidence in unfostered substrains. ChIP-seq affinity zones identified using the HotSpot algorithm 3134 DNaseI HS Hotspots Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwDnase3134RiiiMImmortalHotspotsRep1 3134 H 1 immortalized 3134 DnaseSeq ENCODE Mar 2012 Freeze 2010-07-24 2011-04-23 wgEncodeEM001721 1721 GSM1014196 Stam UW-m Hotspot-v5.1 1 M RIII wgEncodeUwDnase3134RiiiMImmortalHotspotsRep1 Hotspots Immortal cells Mammary DNaseI HS Sequencing Stamatoyannopoulous Stamatoyannopoulous - University of Washington Male High mammary tumor incidence in unfostered substrains. ChIP-seq affinity zones identified using the HotSpot algorithm 3134 DNaseI HS Hotspots Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeq UW RNA-seq GSE39524 RNA-seq from ENCODE/UW Expression and Regulation Description This track was produced as part of the mouse ENCODE Project. This track shows RNA-seq measured genome-wide in mouse tissues and cell lines. Poly-A selected mRNA was used as the source for transcriptome profiling of tissues and cell types that also had corresponding DNase I hypersensitive profiles. 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. Color differences among the views are arbitrary and they provide a visual cue for distinguishing between the different cell and tissue types. This track contains the following views: Plus and Minus SignalsThese views display clusters of overlapping read mappings on the forward and reverse genomic strands. SignalDensity graph (wiggle) of signal enrichment based on processed data. AlignmentsMappings of short 50-base single end reads to the genome. See 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. Fresh tissues were harvested from mice and stored until used for preparing total RNA samples. The total RNA was used as starting material to select poly-A RNA and used for constructing SOLiD libraries according to the protocols supplied by the manufacturer. All RNA samples were spiked in with NIST standards before libraries were constructed. The RNA-seq libraries were sequenced on ABI SOLiD sequencing platform as 50-base reads according to the manufacturer's recommendations. Reads were aligned to the mm9 reference genome using ABI BioScope software version 1.2.1. Colorspace FASTQ format files were created using Heng Li's solid2fastq.pl script version 0.1.4 (Li et al., 2009a), representing 0, 1, 2, 3 color codes with the letters A, C, G, T respectively. Signal files were created from the BAM (Li et al., 2009b) alignments using BEDTools (Quinlan et al., 2010). Release Notes This is Release 1 (July 2012). It contains a total of 25 RNA-seq experiments. Credits These data were generated by the UW ENCODE group. Contact: Richard Sandstrom References Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60. PMID: 19451168; PMC: PMC2705234 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. PMID: 19505943; PMC: PMC2723002 Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. PMID: 20110278; PMC: PMC2832824 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. 
wgEncodeUwRnaSeqViewPlusRawSig Signal RNA-seq from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6PlusRawRep2 Brain E18.5 PR 2 E18.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-30 2012-03-29 wgEncodeEM001997 1997 GSM970875 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6PlusRawRep2 None PlusRawSignal Embryonic day 18.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the plus strand Whole Brain Embryonic day 18.5 RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6PlusRawRep2 Brain E14.5 PR 2 E14.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001995 1995 GSM970874 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6PlusRawRep2 None PlusRawSignal Embryonic day 14.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the plus strand Whole Brain Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6PlusRawRep1 Brain E18.5 PR 1 E18.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-30 2012-03-29 wgEncodeEM001997 1997 GSM970875 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6PlusRawRep1 None PlusRawSignal Embryonic day 18.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the plus strand Whole Brain Embryonic day 18.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6PlusRawRep1 Brain E14.5 PR 1 E14.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001995 1995 GSM970874 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6PlusRawRep1 None PlusRawSignal Embryonic day 14.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the plus strand Whole Brain Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6PlusRawRep2 Thymus 8w PR 2 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002960 2960 GSM970852 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6PlusRawRep2 Pooled PlusRawSignal Adult 8 weeks Thymus Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Thymus Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6PlusRawRep1 Thymus 8w PR 1 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002960 2960 GSM970852 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6PlusRawRep1 Pooled PlusRawSignal Adult 8 weeks Thymus Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Thymus Adult 8 weeks RNA-seq Plus Raw signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6PlusRawRep1 T-Naive 8w PR 1 adult-8wks T-Naive RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002959 2959 GSM970861 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6PlusRawRep1 None PlusRawSignal Adult 8 weeks Naive T cells: CD4+, CD25- Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the plus strand T-Naive Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6PlusRawRep1 Spleen 8w PR 1 adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002958 2958 GSM970860 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6PlusRawRep1 Pooled PlusRawSignal Adult 8 weeks Spleen Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Spleen Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6PlusRawRep2 SkMuscle 8w PR 2 adult-8wks SkMuscle RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002957 2957 GSM970865 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6PlusRawRep2 Pooled PlusRawSignal Adult 8 weeks Skeletal Muscle Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Skeletal Muscle Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6PlusRawRep1 SkMuscle 8w PR 1 adult-8wks SkMuscle RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002957 2957 GSM970865 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6PlusRawRep1 Pooled PlusRawSignal Adult 8 weeks Skeletal Muscle Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Skeletal Muscle Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6PlusRawRep2 Patski PR 2 immortalized Patski RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-23 2012-09-22 wgEncodeEM002950 2950 GSM970866 Stam UW-m coverage cell 1x50 2 polyA F Spretus.BL6-Xist wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6PlusRawRep2 None PlusRawSignal Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Female M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. Graphs the base-by-base density of tags on the plus strand Patski Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6PlusRawRep1 Patski PR 1 immortalized Patski RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-30 2012-03-29 wgEncodeEM002950 2950 GSM970866 Stam UW-m coverage cell 1x50 1 polyA F Spretus.BL6-Xist wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6PlusRawRep1 None PlusRawSignal Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Female M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. Graphs the base-by-base density of tags on the plus strand Patski Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsPlusRawRep2 NIH-3T3 PR 2 immortalized NIH-3T3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM002949 2949 GSM970853 Stam UW-m coverage cell 1x50 2 polyA M NIH/Swiss wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsPlusRawRep2 None PlusRawSignal Immortal cells fibroblast Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Graphs the base-by-base density of tags on the plus strand NIH-3T3 Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsPlusRawRep1 NIH-3T3 PR 1 immortalized NIH-3T3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM002949 2949 GSM970853 Stam UW-m coverage cell 1x50 1 polyA M NIH/Swiss wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsPlusRawRep1 None PlusRawSignal Immortal cells fibroblast Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Graphs the base-by-base density of tags on the plus strand NIH-3T3 Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqMelCellPolyaMImmortalUknPlusRawRep2 MEL PR 2 adult-8wks MEL RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001993 1993 GSM970872 Stam UW-m coverage cell 1x50 2 polyA M Unknown wgEncodeUwRnaSeqMelCellPolyaMImmortalUknPlusRawRep2 None PlusRawSignal Adult 8 weeks Leukemia (K562 analog) Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Unknown strain origin Graphs the base-by-base density of tags on the plus strand MEL Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqMelCellPolyaMImmortalUknPlusRawRep1 MEL PR 1 adult-8wks MEL RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001993 1993 GSM970872 Stam UW-m coverage cell 1x50 1 polyA M Unknown wgEncodeUwRnaSeqMelCellPolyaMImmortalUknPlusRawRep1 None PlusRawSignal Adult 8 weeks Leukemia (K562 analog) Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Unknown strain origin Graphs the base-by-base density of tags on the plus strand MEL Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6PlusRawRep1 Lung 8w PR 1 adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002956 2956 GSM970864 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6PlusRawRep1 Pooled PlusRawSignal Adult 8 weeks Lung Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Lung Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6PlusRawRep2 Lv S_C 8w PR 2 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001992 1992 GSM970873 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6PlusRawRep2 None PlusRawSignal Adult 8 weeks Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the plus strand Liver C57BL6 Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6PlusRawRep1 Lv S_C E14.5 PR 1 E14.5 Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001991 1991 GSM970870 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6PlusRawRep1 None PlusRawSignal Embryonic day 14.5 Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the plus strand Liver C57BL6 Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaME14halfS129PlusRawRep1 Lv S_1 E14.5 PR 1 E14.5 Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-02-13 2012-11-12 wgEncodeEM002961 2961 GSM970851 Stam UW-m coverage cell 1x50 1 polyA M 129 wgEncodeUwRnaSeqLiverCellPolyaME14halfS129PlusRawRep1 Pooled PlusRawSignal Embryonic day 14.5 Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Strain 129, has widely available embryonic stem cells Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Liver 129 Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6PlusRawRep1 Lv S_C 8w PR 1 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001992 1992 GSM970873 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6PlusRawRep1 Pooled PlusRawSignal Adult 8 weeks Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Liver C57BL6 Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6PlusRawRep2 LgInt 8w PR 2 adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002955 2955 GSM970863 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6PlusRawRep2 Pooled PlusRawSignal Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Large Intestine Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6PlusRawRep1 LgInt 8w PR 1 adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002955 2955 GSM970863 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6PlusRawRep1 Pooled PlusRawSignal Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Large Intestine Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6PlusRawRep1 Kidney 8w PR 1 adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001990 1990 GSM970871 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6PlusRawRep1 Pooled PlusRawSignal Adult 8 weeks Kidney Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Kidney Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6PlusRawRep2 Heart 8w PR 2 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002954 2954 GSM970862 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6PlusRawRep2 Pooled PlusRawSignal Adult 8 weeks Heart Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Heart Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6PlusRawRep1 Heart 8w PR 1 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002954 2954 GSM970862 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6PlusRawRep1 Pooled PlusRawSignal Adult 8 weeks Heart Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Heart Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1PlusRawRep1 HlessE E11.5 PR 1 E11.5 HeadlessEmbryo RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001989 1989 GSM970859 Stam UW-m coverage cell 1x50 1 polyA M CD-1 wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1PlusRawRep1 Individual PlusRawSignal Embryonic day 11.5 Whole embryos with heads removed Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from an individual Graphs the base-by-base density of tags on the plus strand HeadlessEmbryo day 11.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6PlusRawRep2 GenitalFP 8w PR 2 adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002953 2953 GSM970869 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6PlusRawRep2 Pooled PlusRawSignal Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand GenitalFatPad Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6PlusRawRep1 GenitalFP 8w PR 1 adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002953 2953 GSM970869 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6PlusRawRep1 Pooled PlusRawSignal Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand GenitalFatPad Adult 8 weeks RNA-seq Plus Raw signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6PlusRawRep1 FatPad 8w PR 1 adult-8wks FatPad RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001988 1988 GSM970858 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6PlusRawRep1 Pooled PlusRawSignal Adult 8 weeks Adipose tissue Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand FatPad Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6PlusRawRep2 Cerebrum 8w PR 2 adult-8wks Cerebrum RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001987 1987 GSM970857 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6PlusRawRep2 Individual PlusRawSignal Adult 8 weeks Cerebrum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Graphs the base-by-base density of tags on the plus strand Cerebrum Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6PlusRawRep1 Cerebrum 8w PR 1 adult-8wks Cerebrum RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001987 1987 GSM970857 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6PlusRawRep1 Pooled PlusRawSignal Adult 8 weeks Cerebrum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Cerebrum Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6PlusRawRep2 Crbellum 8w PR 2 adult-8wks Cerebellum RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-02-13 2012-11-12 wgEncodeEM001986 1986 GSM970856 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6PlusRawRep2 Pooled PlusRawSignal Adult 8 weeks Cerebellum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Cerebellum Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6PlusRawRep1 Crbellum 8w PR 1 adult-8wks Cerebellum RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001986 1986 GSM970856 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6PlusRawRep1 Pooled PlusRawSignal Adult 8 weeks Cerebellum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the plus strand Cerebellum Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6PlusRawRep2 B_(CD43-) 8w PR 2 adult-8wks B-cell_(CD43-) RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002952 2952 GSM970868 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6PlusRawRep2 None PlusRawSignal Adult 8 weeks mouse spleen B cells, CD43-,CD11b- Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the plus strand B-cell (CD43-) Adult 8 weeks RNA-seq Plus Raw signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6PlusRawRep1 B_(CD43-) 8w PR 1 adult-8wks B-cell_(CD43-) RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002952 2952 GSM970868 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6PlusRawRep1 None PlusRawSignal Adult 8 weeks mouse spleen B cells, CD43-,CD11b- Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the plus strand B-cell (CD43-) Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6PlusRawRep1 B_(CD19+) 8w PR 1 adult-8wks B-cell_(CD19+) RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002951 2951 GSM970867 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6PlusRawRep1 None PlusRawSignal Adult 8 weeks B Cell , CD19+ Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the plus strand B-cell (CD19+) Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jPlusRawRep2 416B PR 2 immortalized 416B RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-24 2012-03-24 wgEncodeEM002947 2947 GSM970855 Stam UW-m coverage cell 1x50 2 polyA M B6D2F1/J wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jPlusRawRep2 None PlusRawSignal Immortal cells myeloid progenitor cells, CD34+ Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Graphs the base-by-base density of tags on the plus strand 416B Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jPlusRawRep1 416B PR 1 immortalized 416B RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-24 2012-03-24 wgEncodeEM002947 2947 GSM970855 Stam UW-m coverage cell 1x50 1 polyA M B6D2F1/J wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jPlusRawRep1 None PlusRawSignal Immortal cells myeloid progenitor cells, CD34+ Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Graphs the base-by-base density of tags on the plus strand 416B Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannPlusRawRep2 A20 PR 2 immortalized A20 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002948 2948 GSM970854 Stam UW-m coverage cell 1x50 2 polyA M BALB/cAnN wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannPlusRawRep2 None PlusRawSignal Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male ccMyeloma high incidence H2d Graphs the base-by-base density of tags on the plus strand A20 Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannPlusRawRep1 A20 PR 1 immortalized A20 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM002948 2948 GSM970854 Stam UW-m coverage cell 1x50 1 polyA M BALB/cAnN wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannPlusRawRep1 None PlusRawSignal Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male ccMyeloma high incidence H2d Graphs the base-by-base density of tags on the plus strand A20 Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqViewSignal Signal RNA-seq from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6SigRep2 Brain E18.5 S 2 E18.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-30 2012-03-29 wgEncodeEM001997 1997 GSM970875 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6SigRep2 None Signal Embryonic day 18.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain Embryonic day 18.5 RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6SigRep2 Brain E14.5 S 2 E14.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001995 1995 GSM970874 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6SigRep2 None Signal Embryonic day 14.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6SigRep1 Brain E18.5 S 1 E18.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-30 2012-03-29 wgEncodeEM001997 1997 GSM970875 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6SigRep1 None Signal Embryonic day 18.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain Embryonic day 18.5 RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6SigRep1 Brain E14.5 S 1 E14.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001995 1995 GSM970874 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6SigRep1 None Signal Embryonic day 14.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Signal Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6SigRep2 Thymus 8w S 2 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002960 2960 GSM970852 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6SigRep2 Pooled Signal Adult 8 weeks Thymus Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Thymus Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6SigRep1 Thymus 8w S 1 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002960 2960 GSM970852 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6SigRep1 Pooled Signal Adult 8 weeks Thymus Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Thymus Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6SigRep1 T-Naive 8w S 1 adult-8wks T-Naive RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002959 2959 GSM970861 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6SigRep1 None Signal Adult 8 weeks Naive T cells: CD4+, CD25- Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Signal T-Naive Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6SigRep1 Spleen 8w S 1 adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002958 2958 GSM970860 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6SigRep1 Pooled Signal Adult 8 weeks Spleen Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Spleen Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6SigRep2 SkMuscle 8w S 2 adult-8wks SkMuscle RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002957 2957 GSM970865 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6SigRep2 Pooled Signal Adult 8 weeks Skeletal Muscle Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Skeletal Muscle Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6SigRep1 SkMuscle 8w S 1 adult-8wks SkMuscle RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002957 2957 GSM970865 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6SigRep1 Pooled Signal Adult 8 weeks Skeletal Muscle Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Skeletal Muscle Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6SigRep2 Patski S 2 immortalized Patski RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-23 2012-09-22 wgEncodeEM002950 2950 GSM970866 Stam UW-m coverage cell 1x50 2 polyA F Spretus.BL6-Xist wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6SigRep2 None Signal Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Female M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. Signal Patski Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6SigRep1 Patski S 1 immortalized Patski RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-30 2012-03-29 wgEncodeEM002950 2950 GSM970866 Stam UW-m coverage cell 1x50 1 polyA F Spretus.BL6-Xist wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6SigRep1 None Signal Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Female M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. Signal Patski Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsSigRep2 NIH-3T3 S 2 immortalized NIH-3T3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM002949 2949 GSM970853 Stam UW-m coverage cell 1x50 2 polyA M NIH/Swiss wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsSigRep2 None Signal Immortal cells fibroblast Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Signal NIH-3T3 Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsSigRep1 NIH-3T3 S 1 immortalized NIH-3T3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM002949 2949 GSM970853 Stam UW-m coverage cell 1x50 1 polyA M NIH/Swiss wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsSigRep1 None Signal Immortal cells fibroblast Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Signal NIH-3T3 Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqMelCellPolyaMImmortalUknSigRep2 MEL S 2 adult-8wks MEL RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001993 1993 GSM970872 Stam UW-m coverage cell 1x50 2 polyA M Unknown wgEncodeUwRnaSeqMelCellPolyaMImmortalUknSigRep2 None Signal Adult 8 weeks Leukemia (K562 analog) Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Unknown strain origin Signal MEL Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqMelCellPolyaMImmortalUknSigRep1 MEL S 1 adult-8wks MEL RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001993 1993 GSM970872 Stam UW-m coverage cell 1x50 1 polyA M Unknown wgEncodeUwRnaSeqMelCellPolyaMImmortalUknSigRep1 None Signal Adult 8 weeks Leukemia (K562 analog) Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Unknown strain origin Signal MEL Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6SigRep1 Lung 8w S 1 adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002956 2956 GSM970864 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6SigRep1 Pooled Signal Adult 8 weeks Lung Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Lung Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6SigRep2 Lv S_C 8w S 2 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001992 1992 GSM970873 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6SigRep2 None Signal Adult 8 weeks Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Signal Liver C57BL6 Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6SigRep1 Lv S_C E14.5 S 1 E14.5 Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001991 1991 GSM970870 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6SigRep1 None Signal Embryonic day 14.5 Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Signal Liver C57BL6 Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaME14halfS129SigRep1 Lv S_1 E14.5 S 1 E14.5 Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-02-13 2012-11-12 wgEncodeEM002961 2961 GSM970851 Stam UW-m coverage cell 1x50 1 polyA M 129 wgEncodeUwRnaSeqLiverCellPolyaME14halfS129SigRep1 Pooled Signal Embryonic day 14.5 Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Strain 129, has widely available embryonic stem cells Tissue obtained from pooling samples from various sample organisms Signal Liver 129 Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6SigRep1 Lv S_C 8w S 1 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001992 1992 GSM970873 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6SigRep1 Pooled Signal Adult 8 weeks Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Liver C57BL6 Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6SigRep2 LgInt 8w S 2 adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002955 2955 GSM970863 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6SigRep2 Pooled Signal Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Large Intestine Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6SigRep1 LgInt 8w S 1 adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002955 2955 GSM970863 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6SigRep1 Pooled Signal Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Large Intestine Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6SigRep1 Kidney 8w S 1 adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001990 1990 GSM970871 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6SigRep1 Pooled Signal Adult 8 weeks Kidney Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Kidney Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6SigRep2 Heart 8w S 2 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002954 2954 GSM970862 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6SigRep2 Pooled Signal Adult 8 weeks Heart Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Heart Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6SigRep1 Heart 8w S 1 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002954 2954 GSM970862 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6SigRep1 Pooled Signal Adult 8 weeks Heart Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Heart Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1SigRep1 HlessE E11.5 S 1 E11.5 HeadlessEmbryo RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001989 1989 GSM970859 Stam UW-m coverage cell 1x50 1 polyA M CD-1 wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1SigRep1 Individual Signal Embryonic day 11.5 Whole embryos with heads removed Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from an individual Signal HeadlessEmbryo day 11.5 RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6SigRep2 GenitalFP 8w S 2 adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002953 2953 GSM970869 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6SigRep2 Pooled Signal Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal GenitalFatPad Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6SigRep1 GenitalFP 8w S 1 adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002953 2953 GSM970869 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6SigRep1 Pooled Signal Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal GenitalFatPad Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6SigRep1 FatPad 8w S 1 adult-8wks FatPad RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001988 1988 GSM970858 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6SigRep1 Pooled Signal Adult 8 weeks Adipose tissue Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal FatPad Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6SigRep2 Cerebrum 8w S 2 adult-8wks Cerebrum RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001987 1987 GSM970857 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6SigRep2 Individual Signal Adult 8 weeks Cerebrum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Signal Cerebrum Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6SigRep1 Cerebrum 8w S 1 adult-8wks Cerebrum RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001987 1987 GSM970857 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6SigRep1 Pooled Signal Adult 8 weeks Cerebrum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cerebrum Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6SigRep2 Crbellum 8w S 2 adult-8wks Cerebellum RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-02-13 2012-11-12 wgEncodeEM001986 1986 GSM970856 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6SigRep2 Pooled Signal Adult 8 weeks Cerebellum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cerebellum Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6SigRep1 Crbellum 8w S 1 adult-8wks Cerebellum RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001986 1986 GSM970856 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6SigRep1 Pooled Signal Adult 8 weeks Cerebellum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Signal Cerebellum Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6SigRep2 B_(CD43-) 8w S 2 adult-8wks B-cell_(CD43-) RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002952 2952 GSM970868 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6SigRep2 None Signal Adult 8 weeks mouse spleen B cells, CD43-,CD11b- Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Signal B-cell (CD43-) Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6SigRep1 B_(CD43-) 8w S 1 adult-8wks B-cell_(CD43-) RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002952 2952 GSM970868 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6SigRep1 None Signal Adult 8 weeks mouse spleen B cells, CD43-,CD11b- Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Signal B-cell (CD43-) Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6SigRep1 B_(CD19+) 8w S 1 adult-8wks B-cell_(CD19+) RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002951 2951 GSM970867 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6SigRep1 None Signal Adult 8 weeks B Cell , CD19+ Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Signal B-cell (CD19+) Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jSigRep2 416B S 2 immortalized 416B RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-24 2012-03-24 wgEncodeEM002947 2947 GSM970855 Stam UW-m coverage cell 1x50 2 polyA M B6D2F1/J wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jSigRep2 None Signal Immortal cells myeloid progenitor cells, CD34+ Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Signal 416B Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jSigRep1 416B S 1 immortalized 416B RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-24 2012-03-24 wgEncodeEM002947 2947 GSM970855 Stam UW-m coverage cell 1x50 1 polyA M B6D2F1/J wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jSigRep1 None Signal Immortal cells myeloid progenitor cells, CD34+ Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Signal 416B Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannSigRep2 A20 S 2 immortalized A20 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002948 2948 GSM970854 Stam UW-m coverage cell 1x50 2 polyA M BALB/cAnN wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannSigRep2 None Signal Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male ccMyeloma high incidence H2d Signal A20 Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannSigRep1 A20 S 1 immortalized A20 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM002948 2948 GSM970854 Stam UW-m coverage cell 1x50 1 polyA M BALB/cAnN wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannSigRep1 None Signal Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male ccMyeloma high incidence H2d Signal A20 Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqViewMinusRawSig Signal RNA-seq from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6MinusRawRep2 Brain E18.5 MR 2 E18.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-30 2012-03-29 wgEncodeEM001997 1997 GSM970875 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6MinusRawRep2 None MinusRawSignal Embryonic day 18.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the minus strand Whole Brain Embryonic day 18.5 RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6MinusRawRep2 Brain E14.5 MR 2 E14.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001995 1995 GSM970874 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6MinusRawRep2 None MinusRawSignal Embryonic day 14.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the minus strand Whole Brain Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6MinusRawRep1 Brain E18.5 MR 1 E18.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-30 2012-03-29 wgEncodeEM001997 1997 GSM970875 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6MinusRawRep1 None MinusRawSignal Embryonic day 18.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the minus strand Whole Brain Embryonic day 18.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6MinusRawRep1 Brain E14.5 MR 1 E14.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001995 1995 GSM970874 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6MinusRawRep1 None MinusRawSignal Embryonic day 14.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the minus strand Whole Brain Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6MinusRawRep2 Thymus 8w MR 2 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002960 2960 GSM970852 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6MinusRawRep2 Pooled MinusRawSignal Adult 8 weeks Thymus Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Thymus Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6MinusRawRep1 Thymus 8w MR 1 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002960 2960 GSM970852 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6MinusRawRep1 Pooled MinusRawSignal Adult 8 weeks Thymus Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Thymus Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6MinusRawRep1 T-Naive 8w MR 1 adult-8wks T-Naive RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002959 2959 GSM970861 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6MinusRawRep1 None MinusRawSignal Adult 8 weeks Naive T cells: CD4+, CD25- Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the minus strand T-Naive Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6MinusRawRep1 Spleen 8w MR 1 adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002958 2958 GSM970860 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6MinusRawRep1 Pooled MinusRawSignal Adult 8 weeks Spleen Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Spleen Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6MinusRawRep2 SkMuscle 8w MR 2 adult-8wks SkMuscle RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002957 2957 GSM970865 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6MinusRawRep2 Pooled MinusRawSignal Adult 8 weeks Skeletal Muscle Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Skeletal Muscle Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6MinusRawRep1 SkMuscle 8w MR 1 adult-8wks SkMuscle RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002957 2957 GSM970865 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6MinusRawRep1 Pooled MinusRawSignal Adult 8 weeks Skeletal Muscle Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Skeletal Muscle Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6MinusRawRep2 Patski MR 2 immortalized Patski RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-23 2012-09-22 wgEncodeEM002950 2950 GSM970866 Stam UW-m coverage cell 1x50 2 polyA F Spretus.BL6-Xist wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6MinusRawRep2 None MinusRawSignal Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Female M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. Graphs the base-by-base density of tags on the minus strand Patski Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6MinusRawRep1 Patski MR 1 immortalized Patski RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-30 2012-03-29 wgEncodeEM002950 2950 GSM970866 Stam UW-m coverage cell 1x50 1 polyA F Spretus.BL6-Xist wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6MinusRawRep1 None MinusRawSignal Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Female M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. Graphs the base-by-base density of tags on the minus strand Patski Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsMinusRawRep2 NIH-3T3 MR 2 immortalized NIH-3T3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM002949 2949 GSM970853 Stam UW-m coverage cell 1x50 2 polyA M NIH/Swiss wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsMinusRawRep2 None MinusRawSignal Immortal cells fibroblast Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Graphs the base-by-base density of tags on the minus strand NIH-3T3 Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsMinusRawRep1 NIH-3T3 MR 1 immortalized NIH-3T3 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM002949 2949 GSM970853 Stam UW-m coverage cell 1x50 1 polyA M NIH/Swiss wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsMinusRawRep1 None MinusRawSignal Immortal cells fibroblast Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Graphs the base-by-base density of tags on the minus strand NIH-3T3 Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqMelCellPolyaMImmortalUknMinusRawRep2 MEL MR 2 adult-8wks MEL RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001993 1993 GSM970872 Stam UW-m coverage cell 1x50 2 polyA M Unknown wgEncodeUwRnaSeqMelCellPolyaMImmortalUknMinusRawRep2 None MinusRawSignal Adult 8 weeks Leukemia (K562 analog) Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Unknown strain origin Graphs the base-by-base density of tags on the minus strand MEL Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqMelCellPolyaMImmortalUknMinusRawRep1 MEL MR 1 adult-8wks MEL RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001993 1993 GSM970872 Stam UW-m coverage cell 1x50 1 polyA M Unknown wgEncodeUwRnaSeqMelCellPolyaMImmortalUknMinusRawRep1 None MinusRawSignal Adult 8 weeks Leukemia (K562 analog) Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Unknown strain origin Graphs the base-by-base density of tags on the minus strand MEL Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6MinusRawRep1 Lung 8w MR 1 adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002956 2956 GSM970864 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6MinusRawRep1 Pooled MinusRawSignal Adult 8 weeks Lung Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Lung Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6MinusRawRep2 Lv S_C 8w MR 2 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001992 1992 GSM970873 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6MinusRawRep2 None MinusRawSignal Adult 8 weeks Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the minus strand Liver C57BL6 Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6MinusRawRep1 Lv S_C E14.5 MR 1 E14.5 Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001991 1991 GSM970870 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6MinusRawRep1 None MinusRawSignal Embryonic day 14.5 Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the minus strand Liver C57BL6 Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaME14halfS129MinusRawRep1 Lv S_1 E14.5 MR 1 E14.5 Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-02-13 2012-11-12 wgEncodeEM002961 2961 GSM970851 Stam UW-m coverage cell 1x50 1 polyA M 129 wgEncodeUwRnaSeqLiverCellPolyaME14halfS129MinusRawRep1 Pooled MinusRawSignal Embryonic day 14.5 Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Strain 129, has widely available embryonic stem cells Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Liver 129 Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6MinusRawRep1 Lv S_C 8w MR 1 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001992 1992 GSM970873 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6MinusRawRep1 Pooled MinusRawSignal Adult 8 weeks Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Liver C57BL6 Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6MinusRawRep2 LgInt 8w MR 2 adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002955 2955 GSM970863 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6MinusRawRep2 Pooled MinusRawSignal Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Large Intestine Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6MinusRawRep1 LgInt 8w MR 1 adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002955 2955 GSM970863 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6MinusRawRep1 Pooled MinusRawSignal Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Large Intestine Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6MinusRawRep1 Kidney 8w MR 1 adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001990 1990 GSM970871 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6MinusRawRep1 Pooled MinusRawSignal Adult 8 weeks Kidney Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Kidney Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6MinusRawRep2 Heart 8w MR 2 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002954 2954 GSM970862 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6MinusRawRep2 Pooled MinusRawSignal Adult 8 weeks Heart Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Heart Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6MinusRawRep1 Heart 8w MR 1 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002954 2954 GSM970862 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6MinusRawRep1 Pooled MinusRawSignal Adult 8 weeks Heart Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Heart Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1MinusRawRep1 HlessE E11.5 MR 1 E11.5 HeadlessEmbryo RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001989 1989 GSM970859 Stam UW-m coverage cell 1x50 1 polyA M CD-1 wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1MinusRawRep1 Individual MinusRawSignal Embryonic day 11.5 Whole embryos with heads removed Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from an individual Graphs the base-by-base density of tags on the minus strand HeadlessEmbryo day 11.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6MinusRawRep2 GenitalFP 8w MR 2 adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002953 2953 GSM970869 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6MinusRawRep2 Pooled MinusRawSignal Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand GenitalFatPad Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6MinusRawRep1 GenitalFP 8w MR 1 adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002953 2953 GSM970869 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6MinusRawRep1 Pooled MinusRawSignal Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand GenitalFatPad Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6MinusRawRep1 FatPad 8w MR 1 adult-8wks FatPad RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001988 1988 GSM970858 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6MinusRawRep1 Pooled MinusRawSignal Adult 8 weeks Adipose tissue Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand FatPad Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6MinusRawRep2 Cerebrum 8w MR 2 adult-8wks Cerebrum RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001987 1987 GSM970857 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6MinusRawRep2 Individual MinusRawSignal Adult 8 weeks Cerebrum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Graphs the base-by-base density of tags on the minus strand Cerebrum Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6MinusRawRep1 Cerebrum 8w MR 1 adult-8wks Cerebrum RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001987 1987 GSM970857 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6MinusRawRep1 Pooled MinusRawSignal Adult 8 weeks Cerebrum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Cerebrum Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6MinusRawRep2 Crbellum 8w MR 2 adult-8wks Cerebellum RnaSeq ENCODE Mar 2012 Freeze 2012-03-20 2012-02-13 2012-11-12 wgEncodeEM001986 1986 GSM970856 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6MinusRawRep2 Pooled MinusRawSignal Adult 8 weeks Cerebellum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Cerebellum Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6MinusRawRep1 Crbellum 8w MR 1 adult-8wks Cerebellum RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM001986 1986 GSM970856 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6MinusRawRep1 Pooled MinusRawSignal Adult 8 weeks Cerebellum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Graphs the base-by-base density of tags on the minus strand Cerebellum Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6MinusRawRep2 B_(CD43-) MR 2 adult-8wks B-cell_(CD43-) RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002952 2952 GSM970868 Stam UW-m coverage cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6MinusRawRep2 None MinusRawSignal Adult 8 weeks mouse spleen B cells, CD43-,CD11b- Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the minus strand B-cell (CD43-) Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6MinusRawRep1 B_(CD43-) 8w MR 1 adult-8wks B-cell_(CD43-) RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002952 2952 GSM970868 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6MinusRawRep1 None MinusRawSignal Adult 8 weeks mouse spleen B cells, CD43-,CD11b- Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the minus strand B-cell (CD43-) Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6MinusRawRep1 B_(CD19+) 8w MR 1 adult-8wks B-cell_(CD19+) RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002951 2951 GSM970867 Stam UW-m coverage cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6MinusRawRep1 None MinusRawSignal Adult 8 weeks B Cell , CD19+ Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Graphs the base-by-base density of tags on the minus strand B-cell (CD19+) Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jMinusRawRep2 416B MR 2 immortalized 416B RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-24 2012-03-24 wgEncodeEM002947 2947 GSM970855 Stam UW-m coverage cell 1x50 2 polyA M B6D2F1/J wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jMinusRawRep2 None MinusRawSignal Immortal cells myeloid progenitor cells, CD34+ Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Graphs the base-by-base density of tags on the minus strand 416B Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jMinusRawRep1 416B MR 1 immortalized 416B RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-24 2012-03-24 wgEncodeEM002947 2947 GSM970855 Stam UW-m coverage cell 1x50 1 polyA M B6D2F1/J wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jMinusRawRep1 None MinusRawSignal Immortal cells myeloid progenitor cells, CD34+ Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Graphs the base-by-base density of tags on the minus strand 416B Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannMinusRawRep2 A20 MR 2 immortalized A20 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-12-22 2012-09-22 wgEncodeEM002948 2948 GSM970854 Stam UW-m coverage cell 1x50 2 polyA M BALB/cAnN wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannMinusRawRep2 None MinusRawSignal Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male ccMyeloma high incidence H2d Graphs the base-by-base density of tags on the minus strand A20 Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannMinusRawRep1 A20 MR 1 immortalized A20 RnaSeq ENCODE Mar 2012 Freeze 2012-03-21 2011-06-28 2012-03-28 wgEncodeEM002948 2948 GSM970854 Stam UW-m coverage cell 1x50 1 polyA M BALB/cAnN wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannMinusRawRep1 None MinusRawSignal Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male ccMyeloma high incidence H2d Graphs the base-by-base density of tags on the minus strand A20 Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqViewAlignments Alignments RNA-seq from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6AlnRep2 Brain E18.5 A 2 E18.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-29 wgEncodeEM001997 1997 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6AlnRep2 None Alignments Embryonic day 18.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Shows individual reads mapped to the genome and indicates where bases may mismatch Whole Brain Embryonic day 18.5 RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6AlnRep2 Brain E14.5 A 2 E14.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001995 1995 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6AlnRep2 None Alignments Embryonic day 14.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Shows individual reads mapped to the genome and indicates where bases may mismatch Whole Brain Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6AlnRep1 Brain E18.5 A 1 E18.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-29 wgEncodeEM001997 1997 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6AlnRep1 None Alignments Embryonic day 18.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Shows individual reads mapped to the genome and indicates where bases may mismatch Whole Brain Embryonic day 18.5 RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6AlnRep1 Brain E14.5 A 1 E14.5 WholeBrain RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001995 1995 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6AlnRep1 None Alignments Embryonic day 14.5 Whole Brain Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Shows individual reads mapped to the genome and indicates where bases may mismatch Whole Brain Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6AlnRep2 Thymus 8w A 2 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002960 2960 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6AlnRep2 Pooled Alignments Adult 8 weeks Thymus Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Thymus Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6AlnRep1 Thymus 8w A 1 adult-8wks Thymus RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002960 2960 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6AlnRep1 Pooled Alignments Adult 8 weeks Thymus Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Thymus Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6AlnRep1 T-Naive 8w A 1 adult-8wks T-Naive RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002959 2959 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6AlnRep1 None Alignments Adult 8 weeks Naive T cells: CD4+, CD25- Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Shows individual reads mapped to the genome and indicates where bases may mismatch T-Naive Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6AlnRep1 Spleen 8w A 1 adult-8wks Spleen RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002958 2958 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6AlnRep1 Pooled Alignments Adult 8 weeks Spleen Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Spleen Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6AlnRep2 SkMuscle 8w A 2 adult-8wks SkMuscle RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002957 2957 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6AlnRep2 Pooled Alignments Adult 8 weeks Skeletal Muscle Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Skeletal Muscle Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6AlnRep1 SkMuscle 8w A 1 adult-8wks SkMuscle RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002957 2957 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6AlnRep1 Pooled Alignments Adult 8 weeks Skeletal Muscle Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Skeletal Muscle Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6AlnRep2 Patski A 2 immortalized Patski RnaSeq ENCODE Mar 2012 Freeze 2011-12-23 2012-09-22 wgEncodeEM002950 2950 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA F Spretus.BL6-Xist wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6AlnRep2 None Alignments Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Female M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. Shows individual reads mapped to the genome and indicates where bases may mismatch Patski Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6AlnRep1 Patski A 1 immortalized Patski RnaSeq ENCODE Mar 2012 Freeze 2011-06-30 2012-03-29 wgEncodeEM002950 2950 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA F Spretus.BL6-Xist wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6AlnRep1 None Alignments Immortal cells Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line. Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Female M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. Shows individual reads mapped to the genome and indicates where bases may mismatch Patski Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsAlnRep2 NIH-3T3 A 2 immortalized NIH-3T3 RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM002949 2949 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M NIH/Swiss wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsAlnRep2 None Alignments Immortal cells fibroblast Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Shows individual reads mapped to the genome and indicates where bases may mismatch NIH-3T3 Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsAlnRep1 NIH-3T3 A 1 immortalized NIH-3T3 RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM002949 2949 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M NIH/Swiss wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsAlnRep1 None Alignments Immortal cells fibroblast Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male An outbred Swiss mouse used as a general-purpose stock. Used extensively for pertussis HSF testing. Shows individual reads mapped to the genome and indicates where bases may mismatch NIH-3T3 Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqMelCellPolyaMImmortalUknAlnRep2 MEL A 2 adult-8wks MEL RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001993 1993 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M Unknown wgEncodeUwRnaSeqMelCellPolyaMImmortalUknAlnRep2 None Alignments Adult 8 weeks Leukemia (K562 analog) Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Unknown strain origin Shows individual reads mapped to the genome and indicates where bases may mismatch MEL Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqMelCellPolyaMImmortalUknAlnRep1 MEL A 1 adult-8wks MEL RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001993 1993 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M Unknown wgEncodeUwRnaSeqMelCellPolyaMImmortalUknAlnRep1 None Alignments Adult 8 weeks Leukemia (K562 analog) Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Unknown strain origin Shows individual reads mapped to the genome and indicates where bases may mismatch MEL Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6AlnRep1 Lung 8w A 1 adult-8wks Lung RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002956 2956 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6AlnRep1 Pooled Alignments Adult 8 weeks Lung Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Lung Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6AlnRep2 Lv S_C 8w A 2 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001992 1992 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6AlnRep2 None Alignments Adult 8 weeks Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Shows individual reads mapped to the genome and indicates where bases may mismatch Liver C57BL6 Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6AlnRep1 Lv S_C E14.5 A 1 E14.5 Liver RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001991 1991 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6AlnRep1 None Alignments Embryonic day 14.5 Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Shows individual reads mapped to the genome and indicates where bases may mismatch Liver C57BL6 Embryonic day 14.5 RNA-seq Alignments Rep 1 ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaME14halfS129AlnRep1 Lv S_1 E14.5 A 1 E14.5 Liver RnaSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEM002961 2961 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M 129 wgEncodeUwRnaSeqLiverCellPolyaME14halfS129AlnRep1 Pooled Alignments Embryonic day 14.5 Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Strain 129, has widely available embryonic stem cells Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Liver 129 Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6AlnRep1 Lv S_C 8w A 1 adult-8wks Liver RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001992 1992 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6AlnRep1 Pooled Alignments Adult 8 weeks Liver Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Liver C57BL6 Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6AlnRep2 LgInt 8w A 2 adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002955 2955 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6AlnRep2 Pooled Alignments Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Large Intestine Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6AlnRep1 LgInt 8w A 1 adult-8wks LgIntestine RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002955 2955 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6AlnRep1 Pooled Alignments Adult 8 weeks Large Intestine Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Large Intestine Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6AlnRep1 Kidney 8w A 1 adult-8wks Kidney RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001990 1990 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6AlnRep1 Pooled Alignments Adult 8 weeks Kidney Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Kidney Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6AlnRep2 Heart 8w A 2 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002954 2954 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6AlnRep2 Pooled Alignments Adult 8 weeks Heart Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Heart Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6AlnRep1 Heart 8w A 1 adult-8wks Heart RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002954 2954 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6AlnRep1 Pooled Alignments Adult 8 weeks Heart Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Heart Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1AlnRep1 HlessE E11.5 A 1 E11.5 HeadlessEmbryo RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001989 1989 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M CD-1 wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1AlnRep1 Individual Alignments Embryonic day 11.5 Whole embryos with heads removed Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy. Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch HeadlessEmbryo day 11.5 RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6AlnRep2 GenitalFP 8w A 2 adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002953 2953 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6AlnRep2 Pooled Alignments Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch GenitalFatPad Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6AlnRep1 GenitalFP 8w A 1 adult-8wks GenitalFatPad RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002953 2953 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6AlnRep1 Pooled Alignments Adult 8 weeks Genital Adipose tissue Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch GenitalFatPad Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6AlnRep1 FatPad 8w A 1 adult-8wks FatPad RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001988 1988 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6AlnRep1 Pooled Alignments Adult 8 weeks Adipose tissue Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch FatPad Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6AlnRep2 Cerebrum 8w A 2 adult-8wks Cerebrum RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001987 1987 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6AlnRep2 Individual Alignments Adult 8 weeks Cerebrum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from an individual Shows individual reads mapped to the genome and indicates where bases may mismatch Cerebrum Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6AlnRep1 Cerebrum 8w A 1 adult-8wks Cerebrum RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001987 1987 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6AlnRep1 Pooled Alignments Adult 8 weeks Cerebrum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Cerebrum Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6AlnRep2 Crbellum 8w A 2 adult-8wks Cerebellum RnaSeq ENCODE Mar 2012 Freeze 2012-02-13 2012-11-12 wgEncodeEM001986 1986 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6AlnRep2 Pooled Alignments Adult 8 weeks Cerebellum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Cerebellum Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6AlnRep1 Crbellum 8w A 1 adult-8wks Cerebellum RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM001986 1986 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6AlnRep1 Pooled Alignments Adult 8 weeks Cerebellum Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Tissue obtained from pooling samples from various sample organisms Shows individual reads mapped to the genome and indicates where bases may mismatch Cerebellum Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6AlnRep2 B_(CD43-) 8w A 2 adult-8wks B-cell_(CD43-) RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002952 2952 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M C57BL/6 wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6AlnRep2 None Alignments Adult 8 weeks mouse spleen B cells, CD43-,CD11b- Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Shows individual reads mapped to the genome and indicates where bases may mismatch B-cell (CD43-) Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6AlnRep1 B_(CD43-) 8w A 1 adult-8wks B-cell_(CD43-) RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002952 2952 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6AlnRep1 None Alignments Adult 8 weeks mouse spleen B cells, CD43-,CD11b- Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Shows individual reads mapped to the genome and indicates where bases may mismatch B-cell (CD43-) Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6AlnRep1 B_(CD19+) 8w A 1 adult-8wks B-cell_(CD19+) RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002951 2951 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M C57BL/6 wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6AlnRep1 None Alignments Adult 8 weeks B Cell , CD19+ Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male C57 black 6, the most common inbred strain of laboratory mouse Shows individual reads mapped to the genome and indicates where bases may mismatch B-cell (CD19+) Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jAlnRep2 416B A 2 immortalized 416B RnaSeq ENCODE Mar 2012 Freeze 2011-06-24 2012-03-24 wgEncodeEM002947 2947 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M B6D2F1/J wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jAlnRep2 None Alignments Immortal cells myeloid progenitor cells, CD34+ Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Shows individual reads mapped to the genome and indicates where bases may mismatch 416B Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jAlnRep1 416B A 1 immortalized 416B RnaSeq ENCODE Mar 2012 Freeze 2011-06-24 2012-03-24 wgEncodeEM002947 2947 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M B6D2F1/J wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jAlnRep1 None Alignments Immortal cells myeloid progenitor cells, CD34+ Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male Derived from cross between C57BL/6J Female x DBA/2J Male (C57BL/6xDBA/2)F1. Shows individual reads mapped to the genome and indicates where bases may mismatch 416B Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannAlnRep2 A20 A 2 immortalized A20 RnaSeq ENCODE Mar 2012 Freeze 2011-12-22 2012-09-22 wgEncodeEM002948 2948 Stam UW-m ABI BioScope v1.2.1 cell 1x50 2 polyA M BALB/cAnN wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannAlnRep2 None Alignments Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male ccMyeloma high incidence H2d Shows individual reads mapped to the genome and indicates where bases may mismatch A20 Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW Expression and Regulation 
wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannAlnRep1 A20 A 1 immortalized A20 RnaSeq ENCODE Mar 2012 Freeze 2011-06-28 2012-03-28 wgEncodeEM002948 2948 Stam UW-m ABI BioScope v1.2.1 cell 1x50 1 polyA M BALB/cAnN wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannAlnRep1 None Alignments Immortal cells B cell lymphoma line derived from a spontaneous reticulum cell neoplasm Sequencing analysis of RNA expression Stamatoyannopoulous Stamatoyannopoulous - University of Washington Whole cell Single 50 nt reads Isolated Poly(A) RNA Male ccMyeloma high incidence H2d Shows individual reads mapped to the genome and indicates where bases may mismatch A20 Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW Expression and Regulation 
vegaGeneComposite Vega Genes Vega Annotations Genes and Gene Predictions Description and Methods This track shows gene annotations from the Vertebrate Genome Annotation (Vega) database. Annotations are divided into two subtracks from the Vega Mouse Genome Annotation project: Vega Protein Coding Annotations Vega Annotated Pseudogenes and Immunoglobulin Segments The following information is an excerpt from the Vertebrate Genome Annotation home page: &quot;The Vega database is designed to be a central repository for high-quality, frequently updated manual annotation of different vertebrate finished genome sequence. Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analysed on a clone-by-clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). The annotation is based on supporting evidence only.&quot; &quot;In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery.&quot; Display Conventions and Configuration This track follows the display conventions for gene prediction tracks. Transcript type (and other details) may be found by clicking on the transcript identifier which forms the outside link to the Vega transcript details page. Further information on the gene and transcript classification may be found here. Credits Thanks to Steve Trevanion at the Wellcome Trust Sanger Institute for providing the GTF and FASTA files for the Vega annotations. Vega acknowledgements and publications are listed here. 
vegaPseudoGene Vega Pseudogenes Vega Annotated Pseudogenes and Immunoglobulin Segments Genes and Gene Predictions 
vegaGene Vega Protein Genes Vega Protein Coding Annotations Genes and Gene Predictions 
vistaEnhancersBb VISTA Enhancers VISTA Enhancers Expression and Regulation Description This track shows potential enhancers whose activity was experimentally validated in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. More information can be found on the VISTA Enhancer Browser page. Display Conventions and Configuration Items appearing in red (positive) indicate that a reproducible pattern was observed in the in vivo enhancer assay. Items appearing in blue (negative) indicate that NO reproducible pattern was observed in the in vivo enhancer assay. Note that this annotation refers only to the single developmental timepoint that was tested in this screen (e11.5) and does not exclude the possibility that this region is a reproducible enhancer active at earlier or later timepoints in development. Methods Excerpted from the Vista Enhancer Mouse Enhancer Screen Handbook and Methods page at the Lawrence Berkeley National Laboratory (LBNL) website: Enhancer Candidate Identification Most enhancer candidate sequences are identified by extreme evolutionary sequence conservation or by ChIP-seq. Detailed information related to enhancer identification by extreme evolutionary conservation can be found in the following publications: Pennacchio et al., Genomic strategies to identify mammalian regulatory sequences. Nature Rev Genet 2001 Nobrega et al., Nobrega et al., Scanning human gene deserts for long-range enhancers. Science 2003 Pennacchio et al., In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006 Visel et al., Enhancer identification through comparative genomics. Semin Cell Dev Biol. 2007 Visel et al., Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nature Genet 2008 Detailed information related to enhancer identification by ChIP-seq can be found in the following publications: Visel et al., ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 2009 Visel et al., Genomic views of distant-acting enhancers. Nature 2009 See the Transgenic Mouse Assay section for experimental procedures that were used to perform the transgenic assays: Mouse Enhancer Screen Handbook and Methods UCSC converted the Experimental Data for hg19 and mm9 into bigBed format using the bedToBigBed utility. The data for hg38 was lifted over from hg19. The data for mm10 and mm39 were lifted over from mm9. Data Access VISTA Enhancers data can be explored interactively with the Table Browser and cross-referenced with the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser's REST API. ReMap annotations can be downloaded from the Genome Browser's download server as a bigBed file. This compressed binary format can be remotely queried through command line utilities. Please note that some of the download files can be quite large. Credits Thanks to the Lawrence Berkeley National Laboratory for providing this data References Visel A, Minovitsky S, Dubchak I, Pennacchio LA. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res. 2007 Jan;35(Database issue):D88-92. PMID: 17130149; PMC: PMC1716724 
pubsBingBlat Web Sequences DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research Literature Description This track is powered by Bing! and Microsoft Research. UCSC collaborators at Microsoft Research (Bob Davidson, David Heckerman) implemented a DNA sequence detector and processed thirty days of web crawler updates, which covers roughly 40 billion webpages. The results were mapped with BLAT to the genome. Display Convention and Configuration The track indicates the location of sequences on web pages mapped to the genome, labelled with the web page URL. If the web page includes invisible meta data, then the first author and a year of publication is shown instead of the URL. All matches of one web page are grouped (&quot;chained&quot;) together. Web page titles are shown when you move the mouse cursor over the features. Thicker parts of the features (exons) represent matching sequences, connected by thin lines to matches from the same web page within 30 kbp. The subtrack "individual sequence matches" activates automatically when the user clicks a sequence match and follows the link "Show sequence matches individually" from the details page. Mouse-overs show flanking text around the sequence, and clicking features links to BLAT alignments. - --> Methods All file types (PDFs and various Microsoft Office formats) were converted to text. The results were processed to find groups of words that look like DNA/RNA sequences. These were then mapped with BLAT to the human genome using the same software as used in the Publication track. Credits DNA sequence detection by Bob Davidson at Microsoft Research. HTML parsing and sequence mapping by Maximilian Haeussler at UCSC. References Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM, Open Regulatory Annotation Consortium. Text-mining assisted regulatory annotation. Genome Biol. 2008;9(2):R31. PMID: 18271954; PMC: PMC2374703 Haeussler M, Gerner M, Bergman CM. Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics. 2011 Apr 1;27(7):980-6. PMID: 21325301; PMC: PMC3065681 Van Noorden R. Trouble at the text mine. Nature. 2012 Mar 7;483(7388):134-5. 
pseudoYale60 Yale Pseudo60 Yale Pseudogenes based on Ensembl Release 60 Genes and Gene Predictions Description This track shows pseudogenes identified by the Yale Pseudogene Pipeline. Pseudogenes are defined in this analysis as genomic sequences that are similar to known genes with various inactivating disablements (e.g., premature stop codons or frameshifts) in their &quot;putative&quot; protein coding regions. Pseudogenes are flagged as either recently processed, recently duplicated, or of uncertain origin (either ancient fragments or resulting from a single-exon parent). NOTE: There are 4 pseudogenes missing - these had overlapping coordinates in the blocks representing exons and their identifiers are: PGOMOU00000130313 PGOMOU00000139101 PGOMOU00000136201 PGOMOU00000128816 Methods Briefly, the protein sequences of known human genes (as annotated by Ensembl Release 60) were used to search for similarities, not overlapping with known genes. It was determined whether the matching sequences were disabled copies of genes based on the occurrences of premature stop codons or frameshifts. The intron-exon structure of the functional gene was further used to infer whether a pseudogene was recently duplicated or processed. A duplicated pseudogene retains the intron-exon structure of its parent functional gene, whereas a processed pseudogene shows evidence that this structure has been spliced out. Small pseudogene sequences that cannot be confidently assigned to either the processed or duplicated category may be ancient fragments. Further details are in the references below. Credits These data were generated by the pseudogene annotation group in the Gerstein Lab at Yale University. References More information is available from Pseudogene.org. Zhang Z, Harrison PM, Liu Y, Gerstein M. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res. 2003 Dec;13(12):2541-58. PMID: 14656962; PMC: PMC403796 Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M. Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol. 2005 May 27;349(1):27-45. PMID: 15876366 
allMm9RS_BW GERP GERP scores for mammalian alignments Comparative Genomics Description Genomic Evolutionary Rate Profiling (GERP) is a method for producing position-specific estimates of evolutionary constraint using maximum likelihood evolutionary rate estimation. It also discovers "constrained elements" where multiple positions combine to give a signal that is indicative of a putative functional element; this track shows the position-specific scores only, not the element predictions. Constraint intensity at each individual alignment position is quantified in terms of a "rejected substitutions" (RS) score, defined as the number of substitutions expected under neutrality minus the number of substitutions "observed" at the position. This concept was described, and a first implementation of GERP was presented, in Cooper et al (2005). GERP++ as described in Davydov et al (2010) uses a more rigorous set of algorithms to calculate site-specific RS scores and to discover evolutionarily constrained elements. Sites are scored independently. Positive scores represent a substitution deficit (i.e., fewer substitutions than the average neutral site) and thus indicate that a site may be under evolutionary constraint. Negative scores indicate that a site is probably evolving neutrally; negative scores should not be interpreted as evidence of accelerated rates of evolution because of too many strong confounders, such as alignment uncertainty or rate variance. Positive scores scale with the level of constraint, such that the greater the score, the greater the level of evolutionary constraint inferred to be acting on that site. We applied GERP, as implemented in the GERP++ software package, to quantify the level of evolutionary constraint acting on each site in mm9, based on an alignment of 22 mammals to mm9 with a maximum phylogenetic scope of 4.14 substitutions per neutral site. Gaps in the alignment are treated as missing data, which means that the number of substitutions per neutral site will be less than 4.14 in sites where one or more species has a gap. Thus, RS scores range from a maximum of 4.14 down to a below-zero minimum, which we cap at -8.28. RS scores will vary with alignment depth and level of sequence conservation. A score of 0 indicates that the alignment was too shallow at that position to get a meaningful estimate of constraint. Should classification into "constrained" and "unconstrained" sites be desired, a threshold may be chosen above which sites are considered "constrained". In practice, we find that a RS score threshold of 2 provides high sensitivity while still strongly enriching for truly constrained sites. Methods Given a multiple sequence alignment and a phylogenetic tree with branch lengths representing the neutral rate between the species within that alignment, GERP++ quantifies constraint intensity at each individual position in terms of rejected substitutions, the difference between the neutral rate and the estimated evolutionary rate at the position. GERP++ begins with a pre-defined neutral tree relating the genomes present within the alignment that supplies both the total neutral rate across the entire tree and the relative length of each individual branch. For each alignment column, we estimate a scaling factor, applied uniformly to all branches of the tree, that maximizes the probability of the observed nucleotides in the alignment column. The product of the scaling factor and the neutral rate defines the 'observed' rate of evolution at each position. GERP++ uses the HKY85 model of evolution with the transition/transversion ratio set to 2.0 and nucleotide frequencies estimated from the multiple alignment. To generate RS scores for each position in the mouse genome, we used GERP++ to analyze the TBA alignment of mm9 to 22 other mammalian species (the most distant mammalian species being platypus) spanning over 2.5 billion positions (see the description for the 'Conservation' track for details of this alignment). The alignment was compressed to remove gaps in the human sequence, and GERP++ scores were computed for every position with at least 3 ungapped species present. Importantly, the human sequence was removed from the alignment and not included in either the neutral rate estimation or the site-specific "observed" estimates, and therefore is not included in the RS score. This is consistent with the published work on GERP, and is done to eliminate the confounding influence of deleterious derived alleles segregating in the human population that are present in the reference sequence. The phylogenetic tree used was the generally accepted topology. Neutral branch lengths were estimated from 4-fold degenerate sites in the alignment. Credits The RS scores were generated by David Goode, Dept. of Genetics, Stanford University. GERP++ was developed by Eugene Davydov and Serafim Batzoglou, Dept. of Computer Science, Stanford University; Arend Sidow, Depts. of Pathology and Genetics, Stanford University; and Gregory Cooper, HudsonAlpha Institute for Biotechnology, Huntsville, AL. References Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005 Jul;15(7):901-13. PMID: 15965027; PMC: PMC1172034 Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol. 2010 Dec 2;6(12):e1001025. PMID: 21152010; PMC: PMC2996323 For more information on using GERP to detect putatively functional genetic variation: Cooper GM, Goode DL, Ng SB, Sidow A, Bamshad MJ, Shendure J, Nickerson DA. Single-nucleotide evolutionary constraint scores highlight disease-causing mutations. Nat Methods. 2010 Apr;7(4):250-1. PMID: 20354513; PMC: PMC3145250 Goode DL, Cooper GM, Schmutz J, Dickson M, Gonzales E, Tsai M, Karra K, Davydov E, Batzoglou S, Myers RM et al. Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. Genome Res. 2010 Mar;20(3):301-10. PMID: 20067941; PMC: PMC2840986 
chainNetRn4 Rat Chain/Net Rat (Nov. 2004 (Baylor 3.4/rn4)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rat (Nov. 2004 (Baylor 3.4/rn4)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rat and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rat assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rat/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rat sequence used in this annotation is from the Nov. 2004 (Baylor 3.4/rn4) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rat/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rat chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A56-109-45-137 C-109100-103-45 G-45-103100-109 T-137-45-10956 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetRn4Viewnet Net Rat (Nov. 2004 (Baylor 3.4/rn4)), Chain and Net Alignments Comparative Genomics 
netRn4 Rat Net Rat (Nov. 2004 (Baylor 3.4/rn4)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rat (Nov. 2004 (Baylor 3.4/rn4)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rat and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rat assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rat/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rat sequence used in this annotation is from the Nov. 2004 (Baylor 3.4/rn4) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rat/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rat chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A56-109-45-137 C-109100-103-45 G-45-103100-109 T-137-45-10956 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetRn4Viewchain Chain Rat (Nov. 2004 (Baylor 3.4/rn4)), Chain and Net Alignments Comparative Genomics 
chainRn4 Rat Chain Rat (Nov. 2004 (Baylor 3.4/rn4)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rat (Nov. 2004 (Baylor 3.4/rn4)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rat and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rat assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rat/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rat sequence used in this annotation is from the Nov. 2004 (Baylor 3.4/rn4) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rat/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rat chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A56-109-45-137 C-109100-103-45 G-45-103100-109 T-137-45-10956 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCavPor3 Guinea pig Chain/Net Guinea pig (Feb. 2008 (Broad/cavPor3)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of guinea pig (Feb. 2008 (Broad/cavPor3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both guinea pig and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the guinea pig assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best guinea pig/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The guinea pig sequence used in this annotation is from the Feb. 2008 (Broad/cavPor3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the guinea pig/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single guinea pig chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCavPor3Viewnet Net Guinea pig (Feb. 2008 (Broad/cavPor3)), Chain and Net Alignments Comparative Genomics 
netCavPor3 Guinea pig Net Guinea pig (Feb. 2008 (Broad/cavPor3)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of guinea pig (Feb. 2008 (Broad/cavPor3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both guinea pig and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the guinea pig assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best guinea pig/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The guinea pig sequence used in this annotation is from the Feb. 2008 (Broad/cavPor3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the guinea pig/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single guinea pig chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCavPor3Viewchain Chain Guinea pig (Feb. 2008 (Broad/cavPor3)), Chain and Net Alignments Comparative Genomics 
chainCavPor3 Guinea pig Chain Guinea pig (Feb. 2008 (Broad/cavPor3)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of guinea pig (Feb. 2008 (Broad/cavPor3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both guinea pig and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the guinea pig assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best guinea pig/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The guinea pig sequence used in this annotation is from the Feb. 2008 (Broad/cavPor3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the guinea pig/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single guinea pig chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOryCun2 Rabbit Chain/Net Rabbit (Apr. 2009 (Broad/oryCun2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rabbit (Apr. 2009 (Broad/oryCun2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rabbit and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rabbit assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rabbit/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rabbit sequence used in this annotation is from the Apr. 2009 (Broad/oryCun2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rabbit/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rabbit chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOryCun2Viewnet Net Rabbit (Apr. 2009 (Broad/oryCun2)), Chain and Net Alignments Comparative Genomics 
netOryCun2 Rabbit Net Rabbit (Apr. 2009 (Broad/oryCun2)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rabbit (Apr. 2009 (Broad/oryCun2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rabbit and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rabbit assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rabbit/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rabbit sequence used in this annotation is from the Apr. 2009 (Broad/oryCun2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rabbit/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rabbit chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOryCun2Viewchain Chain Rabbit (Apr. 2009 (Broad/oryCun2)), Chain and Net Alignments Comparative Genomics 
chainOryCun2 Rabbit Chain Rabbit (Apr. 2009 (Broad/oryCun2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rabbit (Apr. 2009 (Broad/oryCun2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rabbit and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rabbit assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rabbit/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rabbit sequence used in this annotation is from the Apr. 2009 (Broad/oryCun2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rabbit/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rabbit chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
laminB1_ES mouse LaminB1 ESC NKI LaminB1 (DamID of LaminB1 in mouse Embryonic Stem cells, log2-ratio) Expression and Regulation Overview Model of chromosome organization in interphase, summarizing the main results presented in this paper. Large, discrete chromosomal domains are dynamically associated with the nuclear lamina (NL), in a manner that is dependent on the cell type (Fig. 7, Peric-Hupkes, et al. 2010). The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. To visualize this process in molecular detail, high-resolution maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem cells were generated via lineage-committed neural precursor (or, neural progenitor) cells into terminally differentiated astrocytes. In addition, genome-nuclear lamina interactions for mouse embryonic fibroblasts were profiled. This revealed that a basal chromosome architecture present in embryonic stem cells is cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal differentiation. This remodeling involves both individual transcription units and multi-gene regions, and affects many genes that determine cellular identity. Often, genes that move away from the lamina are concomitantly activated; many others however remain inactive yet become unlocked for activation in a next differentiation step. These results suggest that lamina-genome interactions are widely involved in the control of gene expression programs during lineage commitment and terminal differentiation. NKI mouse LaminB1 ESC track The mouse LaminB1 ESC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic stem cells. NKI mouse LaminB1 NPC track The mouse LaminB1 NPC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse neural progenitor cells. NKI mouse LaminB1 AC track The mouse LaminB1 AC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse astrocytes. NKI mouse LaminB1 MEF track The mouse LaminB1 MEF track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic fibroblasts. Display Conventions and Configuration The LaminB1 wiggle tracks values range from -6.00 to 4.93. The default vertical viewing range for the wiggle track was chosen from -1.5 to 1.5 because this is roughly +/- 1.5 standard deviations. For an example region see genomic location: chr14:92,000 ,000-96,000,000 (Fig 3A, Peric-Hupkes, Meuleman et al., 2010). Methods The DamID technique was applied to generate high-resolution maps of NL interactions for the entire mouse genome. DamID is based on targeted adenine methylation of DNA sequences that interact in vivo with a protein of interest. DamID was performed as described (Peric-Hupkes, et al. 2010). In short, a fusion protein consisting of Escherichia coli DNA adenine methyltransferase (Dam) fused to mouse LaminB1 was introduced into cultured cells. Dam methylates adenines in the sequence GATC, a mark absent in most eukaryotes. Here, the LaminB1-Dam fusion protein incorporates in the nuclear lamina, as verified by immunofluorescence staining. Hence, the sequences near the nuclear lamina are marked with a unique methylation tag. The adenine methylation pattern was detected with genomic tiling arrays. Unfused Dam was used as a reference. The data shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only. Sample labelling and hybridizations were performed as described (Peric-Hupkes, et al. 2010), on a custom-designed Nimblegen HD2 array, with a median probe spacing of ~1kbp. All probes recognize unique (non-repetitive) sequences. The raw data was log2 transformed and loess normalized, followed by quantile normalization across the single channel data of all hybridizations. Replicate arrays were averaged. Verification The data are based on two independent biological replicates for each cell type, performed on separate days. Fluorescence in situ hybridization microscopy confirmed that most of the LaminB1 associated regions are preferentially located at the nuclear periphery. The array platform, the raw and normalized data have been deposited at the NCBI Gene Expression Omnibus (GEO) under accession number GSE17051. Credits The data for this track were generated by Daan Peric-Hupkes, Wouter Meuleman and Bas van Steensel at the Van Steensel Lab, Netherlands Cancer Institute. References Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gr&#228;f S, Flicek P, Kerkhoven RM, van Lohuizen M et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell. 2010 May 28;38(4):603-13. PMID: 20513434 
laminB1Super NKI Nuc Lamina NKI Nuclear Lamina Associated Domains (LaminB1 DamID) Expression and Regulation Overview Model of chromosome organization in interphase, summarizing the main results presented in this paper. Large, discrete chromosomal domains are dynamically associated with the nuclear lamina (NL), in a manner that is dependent on the cell type (Fig. 7, Peric-Hupkes, et al. 2010). The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. To visualize this process in molecular detail, high-resolution maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem cells were generated via lineage-committed neural precursor (or, neural progenitor) cells into terminally differentiated astrocytes. In addition, genome-nuclear lamina interactions for mouse embryonic fibroblasts were profiled. This revealed that a basal chromosome architecture present in embryonic stem cells is cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal differentiation. This remodeling involves both individual transcription units and multi-gene regions, and affects many genes that determine cellular identity. Often, genes that move away from the lamina are concomitantly activated; many others however remain inactive yet become unlocked for activation in a next differentiation step. These results suggest that lamina-genome interactions are widely involved in the control of gene expression programs during lineage commitment and terminal differentiation. NKI mouse LaminB1 ESC track The mouse LaminB1 ESC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic stem cells. NKI mouse LaminB1 NPC track The mouse LaminB1 NPC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse neural progenitor cells. NKI mouse LaminB1 AC track The mouse LaminB1 AC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse astrocytes. NKI mouse LaminB1 MEF track The mouse LaminB1 MEF track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic fibroblasts. Display Conventions and Configuration The LaminB1 wiggle tracks values range from -6.00 to 4.93. The default vertical viewing range for the wiggle track was chosen from -1.5 to 1.5 because this is roughly +/- 1.5 standard deviations. For an example region see genomic location: chr14:92,000 ,000-96,000,000 (Fig 3A, Peric-Hupkes, Meuleman et al., 2010). Methods The DamID technique was applied to generate high-resolution maps of NL interactions for the entire mouse genome. DamID is based on targeted adenine methylation of DNA sequences that interact in vivo with a protein of interest. DamID was performed as described (Peric-Hupkes, et al. 2010). In short, a fusion protein consisting of Escherichia coli DNA adenine methyltransferase (Dam) fused to mouse LaminB1 was introduced into cultured cells. Dam methylates adenines in the sequence GATC, a mark absent in most eukaryotes. Here, the LaminB1-Dam fusion protein incorporates in the nuclear lamina, as verified by immunofluorescence staining. Hence, the sequences near the nuclear lamina are marked with a unique methylation tag. The adenine methylation pattern was detected with genomic tiling arrays. Unfused Dam was used as a reference. The data shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only. Sample labelling and hybridizations were performed as described (Peric-Hupkes, et al. 2010), on a custom-designed Nimblegen HD2 array, with a median probe spacing of ~1kbp. All probes recognize unique (non-repetitive) sequences. The raw data was log2 transformed and loess normalized, followed by quantile normalization across the single channel data of all hybridizations. Replicate arrays were averaged. Verification The data are based on two independent biological replicates for each cell type, performed on separate days. Fluorescence in situ hybridization microscopy confirmed that most of the LaminB1 associated regions are preferentially located at the nuclear periphery. The array platform, the raw and normalized data have been deposited at the NCBI Gene Expression Omnibus (GEO) under accession number GSE17051. Credits The data for this track were generated by Daan Peric-Hupkes, Wouter Meuleman and Bas van Steensel at the Van Steensel Lab, Netherlands Cancer Institute. References Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gr&#228;f S, Flicek P, Kerkhoven RM, van Lohuizen M et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell. 2010 May 28;38(4):603-13. PMID: 20513434 
chainNetCalJac3 Marmoset Chain/Net Marmoset (March 2009 (WUGSC 3.2/calJac3)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of marmoset (March 2009 (WUGSC 3.2/calJac3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both marmoset and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the marmoset assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best marmoset/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The marmoset sequence used in this annotation is from the March 2009 (WUGSC 3.2/calJac3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the marmoset/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single marmoset chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCalJac3Viewnet Net Marmoset (March 2009 (WUGSC 3.2/calJac3)), Chain and Net Alignments Comparative Genomics 
netCalJac3 Marmoset Net Marmoset (March 2009 (WUGSC 3.2/calJac3)) Alignment net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of marmoset (March 2009 (WUGSC 3.2/calJac3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both marmoset and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the marmoset assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best marmoset/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The marmoset sequence used in this annotation is from the March 2009 (WUGSC 3.2/calJac3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the marmoset/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single marmoset chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCalJac3Viewchain Chain Marmoset (March 2009 (WUGSC 3.2/calJac3)), Chain and Net Alignments Comparative Genomics 
chainCalJac3 Marmoset Chain Marmoset (March 2009 (WUGSC 3.2/calJac3)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of marmoset (March 2009 (WUGSC 3.2/calJac3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both marmoset and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the marmoset assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best marmoset/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The marmoset sequence used in this annotation is from the March 2009 (WUGSC 3.2/calJac3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the marmoset/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single marmoset chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
laminB1_NP mouse LaminB1 NPC NKI LaminB1 (DamID of LaminB1 in mouse Neural Progenitor cells, log2-ratio) Expression and Regulation Overview Model of chromosome organization in interphase, summarizing the main results presented in this paper. Large, discrete chromosomal domains are dynamically associated with the nuclear lamina (NL), in a manner that is dependent on the cell type (Fig. 7, Peric-Hupkes, et al. 2010). The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. To visualize this process in molecular detail, high-resolution maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem cells were generated via lineage-committed neural precursor (or, neural progenitor) cells into terminally differentiated astrocytes. In addition, genome-nuclear lamina interactions for mouse embryonic fibroblasts were profiled. This revealed that a basal chromosome architecture present in embryonic stem cells is cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal differentiation. This remodeling involves both individual transcription units and multi-gene regions, and affects many genes that determine cellular identity. Often, genes that move away from the lamina are concomitantly activated; many others however remain inactive yet become unlocked for activation in a next differentiation step. These results suggest that lamina-genome interactions are widely involved in the control of gene expression programs during lineage commitment and terminal differentiation. NKI mouse LaminB1 ESC track The mouse LaminB1 ESC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic stem cells. NKI mouse LaminB1 NPC track The mouse LaminB1 NPC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse neural progenitor cells. NKI mouse LaminB1 AC track The mouse LaminB1 AC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse astrocytes. NKI mouse LaminB1 MEF track The mouse LaminB1 MEF track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic fibroblasts. Display Conventions and Configuration The LaminB1 wiggle tracks values range from -6.00 to 4.93. The default vertical viewing range for the wiggle track was chosen from -1.5 to 1.5 because this is roughly +/- 1.5 standard deviations. For an example region see genomic location: chr14:92,000 ,000-96,000,000 (Fig 3A, Peric-Hupkes, Meuleman et al., 2010). Methods The DamID technique was applied to generate high-resolution maps of NL interactions for the entire mouse genome. DamID is based on targeted adenine methylation of DNA sequences that interact in vivo with a protein of interest. DamID was performed as described (Peric-Hupkes, et al. 2010). In short, a fusion protein consisting of Escherichia coli DNA adenine methyltransferase (Dam) fused to mouse LaminB1 was introduced into cultured cells. Dam methylates adenines in the sequence GATC, a mark absent in most eukaryotes. Here, the LaminB1-Dam fusion protein incorporates in the nuclear lamina, as verified by immunofluorescence staining. Hence, the sequences near the nuclear lamina are marked with a unique methylation tag. The adenine methylation pattern was detected with genomic tiling arrays. Unfused Dam was used as a reference. The data shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only. Sample labelling and hybridizations were performed as described (Peric-Hupkes, et al. 2010), on a custom-designed Nimblegen HD2 array, with a median probe spacing of ~1kbp. All probes recognize unique (non-repetitive) sequences. The raw data was log2 transformed and loess normalized, followed by quantile normalization across the single channel data of all hybridizations. Replicate arrays were averaged. Verification The data are based on two independent biological replicates for each cell type, performed on separate days. Fluorescence in situ hybridization microscopy confirmed that most of the LaminB1 associated regions are preferentially located at the nuclear periphery. The array platform, the raw and normalized data have been deposited at the NCBI Gene Expression Omnibus (GEO) under accession number GSE17051. Credits The data for this track were generated by Daan Peric-Hupkes, Wouter Meuleman and Bas van Steensel at the Van Steensel Lab, Netherlands Cancer Institute. References Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gr&#228;f S, Flicek P, Kerkhoven RM, van Lohuizen M et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell. 2010 May 28;38(4):603-13. PMID: 20513434 
chainNetRheMac2 Rhesus Chain/Net Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rhesus and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rhesus assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rhesus/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rhesus sequence used in this annotation is from the Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rhesus/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rhesus chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetRheMac2Viewnet Net Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments Comparative Genomics 
netRheMac2 Rhesus Net Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) Alignment net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rhesus and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rhesus assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rhesus/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rhesus sequence used in this annotation is from the Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rhesus/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rhesus chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetRheMac2Viewchain Chain Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments Comparative Genomics 
chainRheMac2 Rhesus Chain Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both rhesus and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the rhesus assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best rhesus/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The rhesus sequence used in this annotation is from the Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the rhesus/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single rhesus chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
laminB1_AC mouse LaminB1 AC NKI LaminB1 (DamID of LaminB1 in mouse Astrocytes, log2-ratio) Expression and Regulation Overview Model of chromosome organization in interphase, summarizing the main results presented in this paper. Large, discrete chromosomal domains are dynamically associated with the nuclear lamina (NL), in a manner that is dependent on the cell type (Fig. 7, Peric-Hupkes, et al. 2010). The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. To visualize this process in molecular detail, high-resolution maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem cells were generated via lineage-committed neural precursor (or, neural progenitor) cells into terminally differentiated astrocytes. In addition, genome-nuclear lamina interactions for mouse embryonic fibroblasts were profiled. This revealed that a basal chromosome architecture present in embryonic stem cells is cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal differentiation. This remodeling involves both individual transcription units and multi-gene regions, and affects many genes that determine cellular identity. Often, genes that move away from the lamina are concomitantly activated; many others however remain inactive yet become unlocked for activation in a next differentiation step. These results suggest that lamina-genome interactions are widely involved in the control of gene expression programs during lineage commitment and terminal differentiation. NKI mouse LaminB1 ESC track The mouse LaminB1 ESC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic stem cells. NKI mouse LaminB1 NPC track The mouse LaminB1 NPC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse neural progenitor cells. NKI mouse LaminB1 AC track The mouse LaminB1 AC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse astrocytes. NKI mouse LaminB1 MEF track The mouse LaminB1 MEF track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic fibroblasts. Display Conventions and Configuration The LaminB1 wiggle tracks values range from -6.00 to 4.93. The default vertical viewing range for the wiggle track was chosen from -1.5 to 1.5 because this is roughly +/- 1.5 standard deviations. For an example region see genomic location: chr14:92,000 ,000-96,000,000 (Fig 3A, Peric-Hupkes, Meuleman et al., 2010). Methods The DamID technique was applied to generate high-resolution maps of NL interactions for the entire mouse genome. DamID is based on targeted adenine methylation of DNA sequences that interact in vivo with a protein of interest. DamID was performed as described (Peric-Hupkes, et al. 2010). In short, a fusion protein consisting of Escherichia coli DNA adenine methyltransferase (Dam) fused to mouse LaminB1 was introduced into cultured cells. Dam methylates adenines in the sequence GATC, a mark absent in most eukaryotes. Here, the LaminB1-Dam fusion protein incorporates in the nuclear lamina, as verified by immunofluorescence staining. Hence, the sequences near the nuclear lamina are marked with a unique methylation tag. The adenine methylation pattern was detected with genomic tiling arrays. Unfused Dam was used as a reference. The data shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only. Sample labelling and hybridizations were performed as described (Peric-Hupkes, et al. 2010), on a custom-designed Nimblegen HD2 array, with a median probe spacing of ~1kbp. All probes recognize unique (non-repetitive) sequences. The raw data was log2 transformed and loess normalized, followed by quantile normalization across the single channel data of all hybridizations. Replicate arrays were averaged. Verification The data are based on two independent biological replicates for each cell type, performed on separate days. Fluorescence in situ hybridization microscopy confirmed that most of the LaminB1 associated regions are preferentially located at the nuclear periphery. The array platform, the raw and normalized data have been deposited at the NCBI Gene Expression Omnibus (GEO) under accession number GSE17051. Credits The data for this track were generated by Daan Peric-Hupkes, Wouter Meuleman and Bas van Steensel at the Van Steensel Lab, Netherlands Cancer Institute. References Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gr&#228;f S, Flicek P, Kerkhoven RM, van Lohuizen M et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell. 2010 May 28;38(4):603-13. PMID: 20513434 
chainNetPonAbe2 Orangutan Chain/Net Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both orangutan and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the orangutan assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best orangutan/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The orangutan sequence used in this annotation is from the July 2007 (WUGSC 2.0.2/ponAbe2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the orangutan/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single orangutan chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPonAbe2Viewnet Net Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)), Chain and Net Alignments Comparative Genomics 
netPonAbe2 Orangutan Net Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Alignment net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both orangutan and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the orangutan assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best orangutan/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The orangutan sequence used in this annotation is from the July 2007 (WUGSC 2.0.2/ponAbe2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the orangutan/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single orangutan chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPonAbe2Viewchain Chain Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)), Chain and Net Alignments Comparative Genomics 
chainPonAbe2 Orangutan Chain Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both orangutan and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the orangutan assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best orangutan/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The orangutan sequence used in this annotation is from the July 2007 (WUGSC 2.0.2/ponAbe2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the orangutan/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single orangutan chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
laminB1_EF mouse LaminB1 MEF NKI LaminB1 (DamID of LaminB1 in mouse Embryonic Fibroblasts, log2-ratio) Expression and Regulation Overview Model of chromosome organization in interphase, summarizing the main results presented in this paper. Large, discrete chromosomal domains are dynamically associated with the nuclear lamina (NL), in a manner that is dependent on the cell type (Fig. 7, Peric-Hupkes, et al. 2010). The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. To visualize this process in molecular detail, high-resolution maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem cells were generated via lineage-committed neural precursor (or, neural progenitor) cells into terminally differentiated astrocytes. In addition, genome-nuclear lamina interactions for mouse embryonic fibroblasts were profiled. This revealed that a basal chromosome architecture present in embryonic stem cells is cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal differentiation. This remodeling involves both individual transcription units and multi-gene regions, and affects many genes that determine cellular identity. Often, genes that move away from the lamina are concomitantly activated; many others however remain inactive yet become unlocked for activation in a next differentiation step. These results suggest that lamina-genome interactions are widely involved in the control of gene expression programs during lineage commitment and terminal differentiation. NKI mouse LaminB1 ESC track The mouse LaminB1 ESC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic stem cells. NKI mouse LaminB1 NPC track The mouse LaminB1 NPC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse neural progenitor cells. NKI mouse LaminB1 AC track The mouse LaminB1 AC track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse astrocytes. NKI mouse LaminB1 MEF track The mouse LaminB1 MEF track shows a high resolution map of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic fibroblasts. Display Conventions and Configuration The LaminB1 wiggle tracks values range from -6.00 to 4.93. The default vertical viewing range for the wiggle track was chosen from -1.5 to 1.5 because this is roughly +/- 1.5 standard deviations. For an example region see genomic location: chr14:92,000 ,000-96,000,000 (Fig 3A, Peric-Hupkes, Meuleman et al., 2010). Methods The DamID technique was applied to generate high-resolution maps of NL interactions for the entire mouse genome. DamID is based on targeted adenine methylation of DNA sequences that interact in vivo with a protein of interest. DamID was performed as described (Peric-Hupkes, et al. 2010). In short, a fusion protein consisting of Escherichia coli DNA adenine methyltransferase (Dam) fused to mouse LaminB1 was introduced into cultured cells. Dam methylates adenines in the sequence GATC, a mark absent in most eukaryotes. Here, the LaminB1-Dam fusion protein incorporates in the nuclear lamina, as verified by immunofluorescence staining. Hence, the sequences near the nuclear lamina are marked with a unique methylation tag. The adenine methylation pattern was detected with genomic tiling arrays. Unfused Dam was used as a reference. The data shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only. Sample labelling and hybridizations were performed as described (Peric-Hupkes, et al. 2010), on a custom-designed Nimblegen HD2 array, with a median probe spacing of ~1kbp. All probes recognize unique (non-repetitive) sequences. The raw data was log2 transformed and loess normalized, followed by quantile normalization across the single channel data of all hybridizations. Replicate arrays were averaged. Verification The data are based on two independent biological replicates for each cell type, performed on separate days. Fluorescence in situ hybridization microscopy confirmed that most of the LaminB1 associated regions are preferentially located at the nuclear periphery. The array platform, the raw and normalized data have been deposited at the NCBI Gene Expression Omnibus (GEO) under accession number GSE17051. Credits The data for this track were generated by Daan Peric-Hupkes, Wouter Meuleman and Bas van Steensel at the Van Steensel Lab, Netherlands Cancer Institute. References Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gr&#228;f S, Flicek P, Kerkhoven RM, van Lohuizen M et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell. 2010 May 28;38(4):603-13. PMID: 20513434 
chainNetPanTro3 Chimp Chain/Net Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of chimp (Oct. 2010 (CGSC 2.1.3/panTro3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both chimp and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the chimp assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best chimp/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The chimp sequence used in this annotation is from the Oct. 2010 (CGSC 2.1.3/panTro3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the chimp/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single chimp chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPanTro3Viewnet Net Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)), Chain and Net Alignments Comparative Genomics 
netPanTro3 Chimp Net Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)) Alignment net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of chimp (Oct. 2010 (CGSC 2.1.3/panTro3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both chimp and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the chimp assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best chimp/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The chimp sequence used in this annotation is from the Oct. 2010 (CGSC 2.1.3/panTro3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the chimp/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single chimp chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPanTro3Viewchain Chain Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)), Chain and Net Alignments Comparative Genomics 
chainPanTro3 Chimp Chain Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of chimp (Oct. 2010 (CGSC 2.1.3/panTro3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both chimp and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the chimp assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best chimp/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The chimp sequence used in this annotation is from the Oct. 2010 (CGSC 2.1.3/panTro3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the chimp/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single chimp chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetHg19 Human Chain/Net Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetHg19Viewnet Net Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments Comparative Genomics 
netHg19 Human Net Human (Feb. 2009 (GRCh37/hg19)) Alignment net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetHg19Viewchain Chain Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments Comparative Genomics 
chainHg19 Human Chain Human (Feb. 2009 (GRCh37/hg19)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best human/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the human/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetAilMel1 Panda Chain/Net Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both panda and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the panda assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best panda/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The panda sequence used in this annotation is from the Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the panda/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single panda chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetAilMel1Viewnet Net Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)), Chain and Net Alignments Comparative Genomics 
netAilMel1 Panda Net Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both panda and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the panda assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best panda/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The panda sequence used in this annotation is from the Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the panda/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single panda chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetAilMel1Viewchain Chain Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)), Chain and Net Alignments Comparative Genomics 
chainAilMel1 Panda Chain Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both panda and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the panda assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best panda/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The panda sequence used in this annotation is from the Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the panda/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single panda chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCanFam2 Dog Chain/Net Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of dog (May 2005 (Broad/canFam2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both dog and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the dog assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best dog/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The dog sequence used in this annotation is from the May 2005 (Broad/canFam2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the dog/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single dog chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCanFam2Viewnet Net Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments Comparative Genomics 
netCanFam2 Dog Net Dog (May 2005 (Broad/canFam2)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of dog (May 2005 (Broad/canFam2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both dog and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the dog assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best dog/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The dog sequence used in this annotation is from the May 2005 (Broad/canFam2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the dog/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single dog chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetCanFam2Viewchain Chain Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments Comparative Genomics 
chainCanFam2 Dog Chain Dog (May 2005 (Broad/canFam2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of dog (May 2005 (Broad/canFam2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both dog and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the dog assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best dog/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The dog sequence used in this annotation is from the May 2005 (Broad/canFam2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the dog/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single dog chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetFelCat4 Cat Chain/Net Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both cat and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the cat assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best cat/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The cat sequence used in this annotation is from the Dec. 2008 (NHGRI/GTB V17e/felCat4) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the cat/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single cat chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetFelCat4Viewnet Net Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)), Chain and Net Alignments Comparative Genomics 
netFelCat4 Cat Net Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both cat and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the cat assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best cat/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The cat sequence used in this annotation is from the Dec. 2008 (NHGRI/GTB V17e/felCat4) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the cat/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single cat chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetFelCat4Viewchain Chain Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)), Chain and Net Alignments Comparative Genomics 
chainFelCat4 Cat Chain Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both cat and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the cat assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best cat/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The cat sequence used in this annotation is from the Dec. 2008 (NHGRI/GTB V17e/felCat4) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the cat/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single cat chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetEquCab2 Horse Chain/Net Horse (Sep. 2007 (Broad/equCab2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of horse (Sep. 2007 (Broad/equCab2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both horse and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the horse assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best horse/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The horse sequence used in this annotation is from the Sep. 2007 (Broad/equCab2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the horse/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single horse chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetEquCab2Viewnet Net Horse (Sep. 2007 (Broad/equCab2)), Chain and Net Alignments Comparative Genomics 
netEquCab2 Horse Net Horse (Sep. 2007 (Broad/equCab2)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of horse (Sep. 2007 (Broad/equCab2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both horse and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the horse assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best horse/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The horse sequence used in this annotation is from the Sep. 2007 (Broad/equCab2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the horse/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single horse chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetEquCab2Viewchain Chain Horse (Sep. 2007 (Broad/equCab2)), Chain and Net Alignments Comparative Genomics 
chainEquCab2 Horse Chain Horse (Sep. 2007 (Broad/equCab2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of horse (Sep. 2007 (Broad/equCab2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both horse and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the horse assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best horse/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The horse sequence used in this annotation is from the Sep. 2007 (Broad/equCab2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the horse/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single horse chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOviAri1 Sheep Chain/Net Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both sheep and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the sheep assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best sheep/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The sheep sequence used in this annotation is from the Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the sheep/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single sheep chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOviAri1Viewnet Net Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)), Chain and Net Alignments Comparative Genomics 
netOviAri1 Sheep Net Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both sheep and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the sheep assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best sheep/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The sheep sequence used in this annotation is from the Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the sheep/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single sheep chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOviAri1Viewchain Chain Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)), Chain and Net Alignments Comparative Genomics 
chainOviAri1 Sheep Chain Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both sheep and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the sheep assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best sheep/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The sheep sequence used in this annotation is from the Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the sheep/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single sheep chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetBosTau6 bosTau6 Chain/Net Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both cow and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the cow assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best cow/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The cow sequence used in this annotation is from the Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the cow/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single cow chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetBosTau6Viewnet Net Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)), Chain and Net Alignments Comparative Genomics 
netBosTau6 Cow Net Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both cow and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the cow assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best cow/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The cow sequence used in this annotation is from the Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the cow/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single cow chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetBosTau6Viewchain Chain Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)), Chain and Net Alignments Comparative Genomics 
chainBosTau6 Cow Chain Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both cow and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the cow assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best cow/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The cow sequence used in this annotation is from the Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the cow/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single cow chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetSusScr2 Pig Chain/Net Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both pig and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the pig assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best pig/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The pig sequence used in this annotation is from the Nov. 2009 (SGSC Sscrofa9.2/susScr2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the pig/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single pig chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetSusScr2Viewnet Net Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)), Chain and Net Alignments Comparative Genomics 
netSusScr2 Pig Net Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both pig and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the pig assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best pig/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The pig sequence used in this annotation is from the Nov. 2009 (SGSC Sscrofa9.2/susScr2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the pig/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single pig chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetSusScr2Viewchain Chain Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)), Chain and Net Alignments Comparative Genomics 
chainSusScr2 Pig Chain Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both pig and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the pig assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best pig/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The pig sequence used in this annotation is from the Nov. 2009 (SGSC Sscrofa9.2/susScr2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the pig/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single pig chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetLoxAfr3 Elephant Chain/Net Elephant (Jul. 2009 (Broad/loxAfr3)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of elephant (Jul. 2009 (Broad/loxAfr3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both elephant and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the elephant assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best elephant/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The elephant sequence used in this annotation is from the Jul. 2009 (Broad/loxAfr3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the elephant/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single elephant chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetLoxAfr3Viewnet Net Elephant (Jul. 2009 (Broad/loxAfr3)), Chain and Net Alignments Comparative Genomics 
netLoxAfr3 Elephant Net Elephant (Jul. 2009 (Broad/loxAfr3)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of elephant (Jul. 2009 (Broad/loxAfr3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both elephant and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the elephant assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best elephant/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The elephant sequence used in this annotation is from the Jul. 2009 (Broad/loxAfr3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the elephant/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single elephant chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetLoxAfr3Viewchain Chain Elephant (Jul. 2009 (Broad/loxAfr3)), Chain and Net Alignments Comparative Genomics 
chainLoxAfr3 Elephant Chain Elephant (Jul. 2009 (Broad/loxAfr3)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of elephant (Jul. 2009 (Broad/loxAfr3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both elephant and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the elephant assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best elephant/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The elephant sequence used in this annotation is from the Jul. 2009 (Broad/loxAfr3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the elephant/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single elephant chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=medium tableSize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMonDom5 Opossum Chain/Net Opossum (Oct. 2006 (Broad/monDom5)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of opossum (Oct. 2006 (Broad/monDom5)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both opossum and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the opossum assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best opossum/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The opossum sequence used in this annotation is from the Oct. 2006 (Broad/monDom5) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the opossum/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single opossum chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMonDom5Viewnet Net Opossum (Oct. 2006 (Broad/monDom5)), Chain and Net Alignments Comparative Genomics 
netMonDom5 Opossum Net Opossum (Oct. 2006 (Broad/monDom5)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of opossum (Oct. 2006 (Broad/monDom5)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both opossum and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the opossum assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best opossum/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The opossum sequence used in this annotation is from the Oct. 2006 (Broad/monDom5) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the opossum/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single opossum chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMonDom5Viewchain Chain Opossum (Oct. 2006 (Broad/monDom5)), Chain and Net Alignments Comparative Genomics 
chainMonDom5 Opossum Chain Opossum (Oct. 2006 (Broad/monDom5)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of opossum (Oct. 2006 (Broad/monDom5)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both opossum and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the opossum assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best opossum/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The opossum sequence used in this annotation is from the Oct. 2006 (Broad/monDom5) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the opossum/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single opossum chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;3000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOrnAna1 Platypus Chain/Net Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both platypus and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the platypus assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best platypus/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The platypus sequence used in this annotation is from the Mar. 2007 (WUGSC 5.0.1/ornAna1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the platypus/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single platypus chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOrnAna1Viewnet Net Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments Comparative Genomics 
netOrnAna1 Platypus Net Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both platypus and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the platypus assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best platypus/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The platypus sequence used in this annotation is from the Mar. 2007 (WUGSC 5.0.1/ornAna1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the platypus/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single platypus chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOrnAna1Viewchain Chain Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments Comparative Genomics 
chainOrnAna1 Platypus Chain Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both platypus and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the platypus assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best platypus/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The platypus sequence used in this annotation is from the Mar. 2007 (WUGSC 5.0.1/ornAna1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the platypus/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single platypus chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetAnoCar2 Lizard Chain/Net Lizard (May 2010 (Broad AnoCar2.0/anoCar2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of lizard (May 2010 (Broad AnoCar2.0/anoCar2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both lizard and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the lizard assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best lizard/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The lizard sequence used in this annotation is from the May 2010 (Broad AnoCar2.0/anoCar2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the lizard/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single lizard chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetAnoCar2Viewnet Net Lizard (May 2010 (Broad AnoCar2.0/anoCar2)), Chain and Net Alignments Comparative Genomics 
netAnoCar2 Lizard Net Lizard (May 2010 (Broad AnoCar2.0/anoCar2)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of lizard (May 2010 (Broad AnoCar2.0/anoCar2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both lizard and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the lizard assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best lizard/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The lizard sequence used in this annotation is from the May 2010 (Broad AnoCar2.0/anoCar2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the lizard/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single lizard chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetAnoCar2Viewchain Chain Lizard (May 2010 (Broad AnoCar2.0/anoCar2)), Chain and Net Alignments Comparative Genomics 
chainAnoCar2 Lizard Chain Lizard (May 2010 (Broad AnoCar2.0/anoCar2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of lizard (May 2010 (Broad AnoCar2.0/anoCar2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both lizard and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the lizard assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best lizard/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The lizard sequence used in this annotation is from the May 2010 (Broad AnoCar2.0/anoCar2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the lizard/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single lizard chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMelGal1 Turkey Chain/Net Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both turkey and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the turkey assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best turkey/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The turkey sequence used in this annotation is from the Dec. 2009 (TGC Turkey_2.01/melGal1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the turkey/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single turkey chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMelGal1Viewnet Net Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)), Chain and Net Alignments Comparative Genomics 
netMelGal1 Turkey Net Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both turkey and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the turkey assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best turkey/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The turkey sequence used in this annotation is from the Dec. 2009 (TGC Turkey_2.01/melGal1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the turkey/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single turkey chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetMelGal1Viewchain Chain Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)), Chain and Net Alignments Comparative Genomics 
chainMelGal1 Turkey Chain Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both turkey and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the turkey assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best turkey/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The turkey sequence used in this annotation is from the Dec. 2009 (TGC Turkey_2.01/melGal1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the turkey/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single turkey chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-114-31-123 C-114100-125-31 G-31-125100-114 T-123-31-11491 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetGalGal3 Chicken Chain/Net Chicken (May 2006 (WUGSC 2.1/galGal3)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of chicken (May 2006 (WUGSC 2.1/galGal3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both chicken and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the chicken assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best chicken/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The chicken sequence used in this annotation is from the May 2006 (WUGSC 2.1/galGal3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the chicken/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single chicken chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetGalGal3Viewnet Net Chicken (May 2006 (WUGSC 2.1/galGal3)), Chain and Net Alignments Comparative Genomics 
netGalGal3 Chicken Net Chicken (May 2006 (WUGSC 2.1/galGal3)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of chicken (May 2006 (WUGSC 2.1/galGal3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both chicken and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the chicken assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best chicken/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The chicken sequence used in this annotation is from the May 2006 (WUGSC 2.1/galGal3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the chicken/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single chicken chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetGalGal3Viewchain Chain Chicken (May 2006 (WUGSC 2.1/galGal3)), Chain and Net Alignments Comparative Genomics 
chainGalGal3 Chicken Chain Chicken (May 2006 (WUGSC 2.1/galGal3)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of chicken (May 2006 (WUGSC 2.1/galGal3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both chicken and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the chicken assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best chicken/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The chicken sequence used in this annotation is from the May 2006 (WUGSC 2.1/galGal3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the chicken/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single chicken chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetXenTro3 X. tropicalis Chain/Net X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both X. tropicalis and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the X. tropicalis assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best X. tropicalis/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The X. tropicalis sequence used in this annotation is from the Nov. 2009 (JGI 4.2/xenTro3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the X. tropicalis/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single X. tropicalis chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetXenTro3Viewnet Net X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)), Chain and Net Alignments Comparative Genomics 
netXenTro3 X. tropicalis Net X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both X. tropicalis and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the X. tropicalis assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best X. tropicalis/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The X. tropicalis sequence used in this annotation is from the Nov. 2009 (JGI 4.2/xenTro3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the X. tropicalis/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single X. tropicalis chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetXenTro3Viewchain Chain X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)), Chain and Net Alignments Comparative Genomics 
chainXenTro3 X. tropicalis Chain X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both X. tropicalis and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the X. tropicalis assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best X. tropicalis/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The X. tropicalis sequence used in this annotation is from the Nov. 2009 (JGI 4.2/xenTro3) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the X. tropicalis/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single X. tropicalis chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetDanRer7 Zebrafish Chain/Net Zebrafish (Jul. 2010 (Zv9/danRer7)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of zebrafish (Jul. 2010 (Zv9/danRer7)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both zebrafish and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the zebrafish assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best zebrafish/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The zebrafish sequence used in this annotation is from the Jul. 2010 (Zv9/danRer7) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the zebrafish/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single zebrafish chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetDanRer7Viewnet Net Zebrafish (Jul. 2010 (Zv9/danRer7)), Chain and Net Alignments Comparative Genomics 
netDanRer7 Zebrafish Net Zebrafish (Jul. 2010 (Zv9/danRer7)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of zebrafish (Jul. 2010 (Zv9/danRer7)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both zebrafish and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the zebrafish assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best zebrafish/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The zebrafish sequence used in this annotation is from the Jul. 2010 (Zv9/danRer7) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the zebrafish/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single zebrafish chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetDanRer7Viewchain Chain Zebrafish (Jul. 2010 (Zv9/danRer7)), Chain and Net Alignments Comparative Genomics 
chainDanRer7 Zebrafish Chain Zebrafish (Jul. 2010 (Zv9/danRer7)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of zebrafish (Jul. 2010 (Zv9/danRer7)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both zebrafish and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the zebrafish assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best zebrafish/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The zebrafish sequence used in this annotation is from the Jul. 2010 (Zv9/danRer7) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the zebrafish/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single zebrafish chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetGasAcu1 Stickleback Chain/Net Stickleback (Feb. 2006 (Broad/gasAcu1)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of stickleback (Feb. 2006 (Broad/gasAcu1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both stickleback and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the stickleback assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best stickleback/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The stickleback sequence used in this annotation is from the Feb. 2006 (Broad/gasAcu1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the stickleback/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single stickleback chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetGasAcu1Viewnet Net Stickleback (Feb. 2006 (Broad/gasAcu1)), Chain and Net Alignments Comparative Genomics 
netGasAcu1 Stickleback Net Stickleback (Feb. 2006 (Broad/gasAcu1)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of stickleback (Feb. 2006 (Broad/gasAcu1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both stickleback and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the stickleback assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best stickleback/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The stickleback sequence used in this annotation is from the Feb. 2006 (Broad/gasAcu1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the stickleback/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single stickleback chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetGasAcu1Viewchain Chain Stickleback (Feb. 2006 (Broad/gasAcu1)), Chain and Net Alignments Comparative Genomics 
chainGasAcu1 Stickleback Chain Stickleback (Feb. 2006 (Broad/gasAcu1)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of stickleback (Feb. 2006 (Broad/gasAcu1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both stickleback and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the stickleback assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best stickleback/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The stickleback sequence used in this annotation is from the Feb. 2006 (Broad/gasAcu1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the stickleback/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single stickleback chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOryLat2 Medaka Chain/Net Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both medaka and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the medaka assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best medaka/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The medaka sequence used in this annotation is from the Oct. 2005 (NIG/UT MEDAKA1/oryLat2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the medaka/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single medaka chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOryLat2Viewnet Net Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)), Chain and Net Alignments Comparative Genomics 
netOryLat2 Medaka Net Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both medaka and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the medaka assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best medaka/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The medaka sequence used in this annotation is from the Oct. 2005 (NIG/UT MEDAKA1/oryLat2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the medaka/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single medaka chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetOryLat2Viewchain Chain Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)), Chain and Net Alignments Comparative Genomics 
chainOryLat2 Medaka Chain Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both medaka and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the medaka assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best medaka/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The medaka sequence used in this annotation is from the Oct. 2005 (NIG/UT MEDAKA1/oryLat2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the medaka/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single medaka chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetFr2 Fugu Chain/Net Fugu (Oct. 2004 (JGI 4.0/fr2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of fugu (Oct. 2004 (JGI 4.0/fr2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both fugu and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the fugu assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best fugu/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The fugu sequence used in this annotation is from the Oct. 2004 (JGI 4.0/fr2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the fugu/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single fugu chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetFr2Viewnet Net Fugu (Oct. 2004 (JGI 4.0/fr2)), Chain and Net Alignments Comparative Genomics 
netFr2 Fugu Net Fugu (Oct. 2004 (JGI 4.0/fr2)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of fugu (Oct. 2004 (JGI 4.0/fr2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both fugu and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the fugu assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best fugu/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The fugu sequence used in this annotation is from the Oct. 2004 (JGI 4.0/fr2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the fugu/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single fugu chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetFr2Viewchain Chain Fugu (Oct. 2004 (JGI 4.0/fr2)), Chain and Net Alignments Comparative Genomics 
chainFr2 Fugu Chain Fugu (Oct. 2004 (JGI 4.0/fr2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of fugu (Oct. 2004 (JGI 4.0/fr2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both fugu and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the fugu assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best fugu/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The fugu sequence used in this annotation is from the Oct. 2004 (JGI 4.0/fr2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the fugu/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single fugu chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetTetNig2 Tetraodon Chain/Net Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both tetraodon and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the tetraodon assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best tetraodon/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The tetraodon sequence used in this annotation is from the Mar. 2007 (Genoscope 8.0/tetNig2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the tetraodon/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single tetraodon chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetTetNig2Viewnet Net Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)), Chain and Net Alignments Comparative Genomics 
netTetNig2 Tetraodon Net Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both tetraodon and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the tetraodon assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best tetraodon/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The tetraodon sequence used in this annotation is from the Mar. 2007 (Genoscope 8.0/tetNig2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the tetraodon/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single tetraodon chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetTetNig2Viewchain Chain Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)), Chain and Net Alignments Comparative Genomics 
chainTetNig2 Tetraodon Chain Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both tetraodon and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the tetraodon assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best tetraodon/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The tetraodon sequence used in this annotation is from the Mar. 2007 (Genoscope 8.0/tetNig2) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the tetraodon/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single tetraodon chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPetMar1 Lamprey Chain/Net Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both lamprey and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the lamprey assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best lamprey/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The lamprey sequence used in this annotation is from the Mar. 2007 (WUGSC 3.0/petMar1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the lamprey/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single lamprey chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPetMar1Viewnet Net Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)), Chain and Net Alignments Comparative Genomics 
netPetMar1 Lamprey Net Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both lamprey and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the lamprey assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best lamprey/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The lamprey sequence used in this annotation is from the Mar. 2007 (WUGSC 3.0/petMar1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the lamprey/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single lamprey chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetPetMar1Viewchain Chain Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)), Chain and Net Alignments Comparative Genomics 
chainPetMar1 Lamprey Chain Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both lamprey and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the lamprey assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best lamprey/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The lamprey sequence used in this annotation is from the Mar. 2007 (WUGSC 3.0/petMar1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the lamprey/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single lamprey chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetBraFlo1 Lancelet Chain/Net Lancelet (Mar. 2006 (JGI 1.0/braFlo1)), Chain and Net Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of lancelet (Mar. 2006 (JGI 1.0/braFlo1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both lancelet and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the lancelet assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best lancelet/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The lancelet sequence used in this annotation is from the Mar. 2006 (JGI 1.0/braFlo1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the lancelet/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single lancelet chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetBraFlo1Viewnet Net Lancelet (Mar. 2006 (JGI 1.0/braFlo1)), Chain and Net Alignments Comparative Genomics 
netBraFlo1 Lancelet Net Lancelet (Mar. 2006 (JGI 1.0/braFlo1)) Alignment Net Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of lancelet (Mar. 2006 (JGI 1.0/braFlo1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both lancelet and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the lancelet assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best lancelet/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The lancelet sequence used in this annotation is from the Mar. 2006 (JGI 1.0/braFlo1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the lancelet/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single lancelet chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961 
chainNetBraFlo1Viewchain Chain Lancelet (Mar. 2006 (JGI 1.0/braFlo1)), Chain and Net Alignments Comparative Genomics 
chainBraFlo1 Lancelet Chain Lancelet (Mar. 2006 (JGI 1.0/braFlo1)) Chained Alignments Comparative Genomics Description This track shows regions of the genome that are alignable to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns. Chain Track The chain track shows alignments of lancelet (Mar. 2006 (JGI 1.0/braFlo1)) to the mouse genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both lancelet and mouse simultaneously. These &quot;double-sided&quot; gaps can be caused by local inversions and overlapping deletions in both species. The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the lancelet assembly or an insertion in the mouse assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the mouse genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. In the &quot;pack&quot; and &quot;full&quot; display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment. Net Track The net track shows the best lancelet/mouse chain for every part of the mouse genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The lancelet sequence used in this annotation is from the Mar. 2006 (JGI 1.0/braFlo1) assembly. Display Conventions and Configuration Chain Track By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the &quot;off&quot; button next to: Color track based on chromosome. To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome. Net Track In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth. In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement. Individual items in the display are categorized as one of four types (other than gap): Top - the best, longest match. Displayed on level 1. Syn - line-ups on the same chromosome as the gap in the level above it. Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation. NonSyn - a match to a chromosome different from the gap in the level above. Methods Chain track Transposons that have been inserted since the lancelet/mouse split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single lancelet chromosome and a single mouse chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used: &nbsp;ACGT A91-90-25-100 C-90100-100-25 G-25-100100-90 T-100-25-9091 Chains scoring below a minimum score of &quot;5000&quot; were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain: -linearGap=loose tablesize 11 smallSize 111 position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 Net track Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. Credits Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison. Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program. The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler. The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent. The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent. References Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961