This track displays biosample-specific candidate cis-regulatory elements (cCREs) alongside genome-wide epigenomic signals for the ENCODE Core Collection of 170 ENCODE biosamples that have been fully profiled using four core assays: DNase-seq, ChIP-seq for the histone modifications H3K4me3 and H3K27ac, and ChIP-seq for CTCF binding.
Each subtrack corresponds to an individual experiment in a specific biosample. These data form the basis for generating biosample-specific annotations of cCREs, which compose the fifth subtrack for the biosample.
Additional epigenomic datasets are available at the ENCODE portal, and further exploration of cCREs and their supporting data is available through the SCREEN web tool, accessible via the track details page.
Each biosample contains five subtracks (DNase, CTCF, H3K27ac, and H3K4me3 signals and biosample-specific cCREs). Click a specific biosample type and organ/tissue combination to view available datasets. Epigenomic subtracks can be further filtered by the signal type. Below is a graphic summarizing biosampling available:
Each signal track is colored based on the type of signal. The cCREs subtrack displays each active cCRE in the corresponding biosample as a colored box by type
For item sin the cCREs track, mousing over shows the element ID, along with a linkout to the corresponding element on SCREEN, as well as the cCRE group and Classification type.
The DNase-seq data were processed using the ENCODE DNase-seq pipeline, the H3K4me3 and H3K27ac ChIP-seq data were processed using the ENCODE histone ChIP-seq pipeline, and the CTCF ChIP-seq data were processed using the ENCODE transcription factor ChIP-seq pipeline.
In addition to the cell type-agnostic classification (described in the cCRE Registry track in this collection), we evaluated the biochemical activity of each cCRE in individual biosamples using the corresponding biosample-specific DNase, H3K4me3, H3K27ac, and CTCF data. This allowed us to annotate active cCREs in individual biosamples, included as the cCRE subtrack for each biosample. cCREs with low DNase Z-scores in individual biosamples were deemed to be inactive and labeled with "Low Chromatin Accessibility."
All data is available from the ENCODE data portal.
The data on the UCSC Genome Browser can be explored interactively with the Table Browser or the Data Integrator. For automated download and analysis, the genome annotation is stored at UCSC in bigWig and bigBed files that can be downloaded from our download server.
The cCREs tracks in this data are found as bigBed files, and the biosignal tracks as bigWig files.
See the Data format link besides the specific data track for a URL to the file on our download
server. Individual
regions or the whole genome annotation can be obtained using our tools bigWigToWig
or bigBedToBed which can be compiled from the source code or downloaded as a precompiled
binary for your system. Instructions for downloading source code and binaries can be found
here.
The tools can also be used to obtain features confined to a given range, e.g.,
bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 https://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4/ccre/coreCollection/ENCFF811RQX.bw stdout
or
bigBedToBed -chrom=chr1 -start=100000 -end=100500 https://hgdownload.soe.ucsc.edu/gbdb/hg38/encode4/ccre/coreCollection/ENCFF013UBZ_ENCFF901QWB_ENCFF972ZHA_ENCFF500RDL.bb stdout
Data were generated by the ENCODE Consortium. We thank the production labs for generating the data: Drs. Barbara Wold (Caltech), Bing Ren (UCSD), Bradley Bernstein (Broad), Gregory Crawford (Duke), John Stamatoyannopoulos (UW), Joseph Costello (UCSF), Michael Snyder Lab (Stanford), Peggy Farnham (USC), Richard Myers (HAIB), Stephen Montgomery (Stanford), Vishwanath Iyer (UTA), Will Greenleaf (Stanford), and Yin Shen (UCSF).
The data were further processed for visualization through a collaborative effort between the Weng lab and the Moore lab at UMass Chan Medical School (funded by NIH grant HG012343). Integration and visualization were developed by Drs. Mingshi Gao, Jill Moore, and Zhiping Weng at UMass Chan Medical School, who were part of the ENCODE Data Analysis Center. We thank the ENCODE production labs for generating the data.
ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 Jul;583(7818):699-710. PMID: 32728249; PMC: PMC7410828
Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y et al. An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation. bioRxiv. 2024 Dec 26;. PMID: 39763870; PMC: PMC11703161