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Description
The ENCODE project has established an epigenomic resource for mammalian development,
profiling a diverse panel of mouse tissues at eight developmental stages from 10.5 days post
conception until birth.
This track set presents the results of a comprehensive study of chromatin
state across these developmental stages, based on 1,128 ChiP-seq assays of 8 histone modifications
in 12 tissues, performed by the
laboratory of Bing Ren
as part of the ENCODE Consortium, phase 3.
Histone modifications are post-translational chemical modifications (e.g. methylation,
acetylation) of histone proteins present in chromatin. Histone modifications are core
components of a cell's epigenome, and influence gene expression by modulating the activity of
DNA sequences.
Display Conventions and Configuration
This track is a multi-view composite track that contains two 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 views in this track are:
- Peaks
- Regions of statistically significant signal
enrichment
- Signal
- Density graph of signal enrichment.
Peaks displayed in this track set are replicated peaks called with the
Irreproducible Discovery Rate (IDR) framework
These peaks are identical to those in the "replicated peaks" files
on the ENCODE data portal.
Signals displayed in this track correspond to the "fold change
over control" files from merged replicates, reflecting the fold enrichment of ChIP signal over
the input control. Data for individual replicates are available through the
ENCODE portal.
Tracks are colored by histone modification. The table below list shows the assigned track color
and the genomic region type and activity level characteristic of each modification.
| Modification | | Color | Regions | Activity Level |
|---|
| H3K4me3 | |
| dark blue |
promoters | active, poised |
| H3K4me2 | |
| royal blue |
promoters, enhancers | active, poised |
| H3K4me1 | | | light blue |
enhancers | active, poised |
| H3K27ac | |
| dark green |
promoters, enhancers | active |
| H3K9ac | |
| light green |
promoters, enhancers | active |
| H3K36me3 | |
| gold |
exons | active |
| H3K27me3 | |
| dark red |
introns, intergenic | repressed |
| H3K9me3 | |
| light red |
heterochromatin | repressed |
Methods
ChIP-seq data generation
ChIP-seq experiments for all marks and tissues from E11.5 - P0 were performed
as described in Shen et. al 2012 (see References below).
The ChIP-seq protocol was modified slightly for all E10.5
experiments due to the low amount of input ("micro" ChIP-seq).
Detailed protocols for both standard and micro ChIP-seq are available from the ENCODE
project portal (see Data Access section, below).
ChIP-seq antibodies
A full list of antibodies used by the Ren Lab for ENCODE can be found
here. The antibody catalog and lot numbers are available for each experiment on the
ENCODE portal.
ChIP-seq data processing
ChIP-seq data were analyzed using a software pipeline implemented by the ENCODE Data
Coordinating Center (DCC) for the ENCODE Consortium. Each step of the pipeline corresponds
to a script written in the Python programming language that assembles the input files, runs
external programs, and calculates quality-control metrics. The ENCODE histone ChIP-seq pipeline
is among the collection of ENCODE Uniform Processing Pipelines that can be found
here.
ChIP-seq peak calling
Replicated peaks were called using an approach based on
Irreproducible Discovery Rate
to ensure an adequate sampling of noise for subsequent replicate comparisons.
Briefly, peaks were initially called at a relaxed p-value threshold of 1 x 10-2.
Such relaxed peak sets were generated for each biological replicate, for the replicates pooled,
and for pooled pseudoreplicates of each true replicate (each pseudoreplicate consists of half
the reads sampled without replacement).
Peaks from the pooled replicate set were retained in the replicated peak set if they overlapped
by at least half their length (in bases) peaks from both biological replicates.
Additionally, peaks that overlapped both pooled pseudoreplicates were added to the replicated
peak set.
In this way very strong biological replicates "rescue" peaks that were only marginal in a second replicate.
Data Access
Data from this and all phases of ENCODE are publicly available through the
ENCODE portal.
The specific experiments included in this track set are listed
here.
Credits
Thanks to David Gorkin and Yanxiao Zhang at the Ren lab (UCSD/Ludwig Institute for Cancer Research)
and Iros Barozzi of the Environmental Genomics and Systems Biology Division
at the Lawrence Berkeley National Laboratory for providing this data and assisting with track development at UCSC.
References
Gorkin et al. An atlas of dynamic chromatin landscapes in the developing mouse fetus.
Nature, In Press. (pre-print: doi:
https://doi.org/10.1101/166652)
Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee
BT et al.
ENCODE data at the ENCODE portal.
Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32.
PMID: 26527727; PMC: PMC4702836
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV et
al.
A map of the cis-regulatory sequences in the mouse genome.
Nature. 2012 Aug 2;488(7409):116-20.
PMID: 22763441; PMC: PMC4041622
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