ENCODE Regulation Histone Modifications Track Settings
 
Histone modifications in embryonic tissue (8 marks, 12 tissues, 8 ages) from ChIP-seq by ENCODE 3 (UCSD/Ren)

Track collection: Integrated Regulation from ENCODE

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 Configure 		 forebrain  H3K4me3      E15.5  Signal  ChIP-seq signal of embryonic forebrain H3K4me3 on day E15.5 from ENCODE 3 (UCSD/Ren)   Data format 
 
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 Configure 		 forebrain  H3K4me2      E15.5  Signal  ChIP-seq signal of embryonic forebrain H3K4me2 on day E15.5 from ENCODE 3 (UCSD/Ren)   Data format 
 
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 Configure 		 forebrain  H3K4me1      E15.5  Signal  ChIP-seq signal of embryonic forebrain H3K4me1 on day E15.5 from ENCODE 3 (UCSD/Ren)   Data format 
 
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 Configure 		 forebrain  H3K27ac      E15.5  Signal  ChIP-seq signal of embryonic forebrain H3K27ac on day E15.5 from ENCODE 3 (UCSD/Ren)   Data format 
 
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 Configure 		 forebrain  H3K9ac      E15.5  Signal  ChIP-seq signal of embryonic forebrain H3K9ac on day E15.5 from ENCODE 3 (UCSD/Ren)   Data format 
 
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 Configure 		 forebrain  H3K36me3      E15.5  Signal  ChIP-seq signal of embryonic forebrain H3K36me3 on day E15.5 from ENCODE 3 (UCSD/Ren)   Data format 
 
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 Configure 		 forebrain  H3K27me3      E15.5  Signal  ChIP-seq signal of embryonic forebrain H3K27me3 on day E15.5 from ENCODE 3 (UCSD/Ren)   Data format 
 
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 Configure 		 forebrain  H3K9me3      E15.5  Signal  ChIP-seq signal of embryonic forebrain H3K9me3 on day E15.5 from ENCODE 3 (UCSD/Ren)   Data format 
    
Assembly: Mouse Dec. 2011 (GRCm38/mm10)

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 ColorRegionsActivity 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