Description
This track displays maps of chromatin state of ENCODE cell types. Chemical
modifications (methylation, acylation) to the histone proteins present
in chromatin influence gene expression by changing how accessible the
chromatin is to transcription.
The ChIP-seq method involves cross-linking histones and other DNA
associated proteins to genomic DNA within cells using formaldehyde. The
cross-linked chromatin is subsequently extracted, mechanically sheared,
and immunoprecipitated using specific antibodies. After reversal of
cross-links, the immunoprecipitated DNA is sequenced and mapped to the
human reference genome. The relative enrichment of each antibody-target
(epitope) across the genome is inferred from the density of mapped
fragments.
Display Conventions
These tracks are multi-view composite tracks that contains multiple
data types (views). For each view, there are multiple subtracks that
display individually on the browser. Each view within each track
has separate display controls, as described here.
Specific
aspects
of the views vary by track. The views
include:
Peaks
Regions of significant ChIP-Seq
affinity.
Signal
The density of tags mapping within a
sliding window.
Raw Signal
Density graph (wiggle) of signal
enrichment based on aligned read density.
Credits
These data were generated and analyzed as part of the ENCODE project, a
genome-wide consortium project with the aim of cataloging all
functional elements in the human genome. This effort includes
collecting a variety of data over a specific set of cell types.
Consequently,
data
related
to these tracks be available under ENCODE
tracks.
References
Segal E, Widom J. What controls nucleosome positions?
Trends
Genet.
2009 Aug;25(8):335-43.
Geiman TM, Robertson KD. Chromatin remodeling, histone
modifications, and DNA methylation-how does it all fit together?
J
Cell
Biochem. 2002;87(2):117-25.
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consent, submit publications that use an unpublished ENCODE dataset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.