Schema for Open Chromatin - Open chromatin in embryonic tissue (12 tissues, 8 ages) from ATAC-seq by ENCODE 3 (UCSD/Ren)
  Database: mm10    Primary Table: encode3RenAtacPeakLimbE11 Data last updated: 2019-09-09
Big Bed File Download: /gbdb/mm10/encode3/atac/encode3RenAtacPeakLimbE11.bb
Item Count: 165,336
Format description: Browser Extensible Data
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart130337901Start position in chromosome
chromEnd130338030End position in chromosome
namepeak_6914Name of item.
score28Score (0-1000)

Sample Rows
 
chromchromStartchromEndnamescore
chr1130337901130338030peak_691428
chr1130340685130340783peak_691535
chr1130346904130347059peak_691635
chr1130348663130348777peak_691722
chr1130350322130350550peak_691842
chr1130370966130371039peak_691935
chr1130372061130372134peak_692047
chr1130372367130372440peak_692153
chr1130378435130378508peak_692222
chr1130409723130409895peak_692342

Open Chromatin (encode3RenAtac) 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 accessibility across these developmental stages, based on 122 ATAC-seq assays in 12 tissues performed by the laboratory of Bing Ren as part of the ENCODE Consortium, phase 3.

ATAC-seq profiles "open" or "accessible" chromatin that is relatively devoid of packaging nucleosome particles. This chromatin accesibility is characteristic of active and poised cis regulatory elements, and makes the underlying DNA more amenable to the binding of transcription factors, which can function in turn to recruit co-factors and influence transcriptional activity.

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 called on data merged between two biological replicates. Signals displayed in this track correspond to the "fold change over background" files from merged replicates. Data for individual replicates are available through the ENCODE portal and the Ren Lab Website.

Methods

ATAC-seq data generation

ATAC-seq was performed as described in Buenrostro et al. 2013 (see References below), with modifications to optimize for frozen tissue. The complete ATAC-seq protocol is available via the ENCODE data portal here.

ATAC-seq data processing

ATAC-seq reads were trimmed with a custom adapter script and mapped to mm10 using bowtie version 2.2.6 and samtools version 1.2 to eliminate PCR duplicates. MACS2 version 2.1.1.20160309 was used for generating signal tracks and peak calling with the following parameters:

-nomodel -shift 37 -ext 73 -pval 1e-2 -B -SPMR -call-summits

To produce a set of "replicated" ATAC-seq peaks for analysis, the peak calling steps above were performed for each pair of replicates independently as well as a pooled set of data from both replicates. The intersectBed tool from the bedtools v2.27.1 suite was used to identify a set of replicated peaks, defined as the subset of peaks from the pooled set that are present independently in both replicate peak call sets.

Data Access

Experiments included in this track set are available from the ENCODE portal here.

Credits

Thanks to David Gorkin, Yuan Zhao and Yanxiao Zhang at the Ren lab (UCSD/Ludwig Institute for Cancer Research) for providing this data and assisting with track development at UCSC.

References

Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013 Dec;10(12):1213-8. PMID: 24097267; PMC: PMC3959825

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