Schema for Histone Modifications - Histone modifications in embryonic tissue (8 marks, 12 tissues, 8 ages) from ChIP-seq by ENCODE 3 (UCSD/Ren)
  Database: mm10    Primary Table: encode3Ren_hindbrain_H3K4me1_E11 Data last updated: 2019-02-10
Big Bed File Download: /gbdb/mm10/encode3/histones/ENCFF062LZU.bigBed
Item Count: 40,579
Format description: BED6+4 Peaks of signal enrichment based on pooled, normalized (interpreted) data.
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart131073608Start position in chromosome
chromEnd131073800End position in chromosome
namePeak_35824Name given to a region (preferably unique). Use . if no name is assigned
score118Indicates how dark the peak will be displayed in the browser (0-1000)
strand.+ or - or . for unknown
signalValue3.22784Measurement of average enrichment for the region
pValue4.14638Statistical significance of signal value (-log10). Set to -1 if not used.
qValue1.39645Statistical significance with multiple-test correction applied (FDR -log10). Set to -1 if not used.
peak53Point-source called for this peak; 0-based offset from chromStart. Set to -1 if no point-source called.

Sample Rows
 
chromchromStartchromEndnamescorestrandsignalValuepValueqValuepeak
chr1131073608131073800Peak_35824118.3.227844.146381.3964553
chr1131079017131079593Peak_11725206.4.029145.892142.45470331
chr1131083809131084161Peak_8777248.4.190886.627842.93075158
chr1131086544131087175Peak_27431134.3.439364.495501.53681169
chr1131096126131096420Peak_4389092.2.996793.669781.09848156
chr1131098470131098835Peak_28053134.3.282834.430671.4756720
chr1131134779131134976Peak_26791139.3.470794.546851.5734893
chr1131137041131137275Peak_28054134.3.282834.430671.47567125
chr1131239647131239862Peak_4569287.2.757653.534120.98749128
chr1131240601131240818Peak_28055134.3.282834.430671.47567117

Histone Modifications (encode3RenHistone) Track Description
 

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