Overview

This trackhub contains signal and peaks produced by the ENCODE Consortium for assays related to DNA and associated factors. Included assays profile DNA accessibility, nucleosome positioning, DNA binding by transcription factors, and DNA replication patterns. The peaks in this trackhub constitute a component of the ground level of the ENCODE Encyclopedia. All data included in this trackhub were produced by ENCODE uniform processing pipelines for the relevant assays and are publicly available at the ENCODE Portal. The hub is updated periodically as new data become available. This hub contains data mapped to hg19, GRCh38, and mm10.

The data in this hub are grouped into tracks by assay. Data within tracks are grouped by biosample. Data from ChIP-seq experiments are also available in tracks grouped by ChIP target instead. Additionally, there is an "Experiments by Ontology" track which groups data from all assays by tissue ontology information associated with the biosample as provided at the ENCODE Portal.

This trackhub contains ground-level output from the ENCODE uniform processing pipelines per experiment only. Integrated data, such as candidate regulatory elements, transcription factor motif sites, and other higher-level annotations are available in separate trackhubs.

Available assays

The following assays have data available:

• DNase-seq (hg19, GRCh38, mm10): profiles DNA accessibility. Available data types include hotspots, peaks, and read-depth normalized signal. See the DNase-seq computational pipeline overview for more information.
• ATAC-seq (GRCh38, mm10): profiles DNA accessibility. Available data types include unreplicated and replicated fold change signal and peaks. See the ATAC-seq computational pipeline overview for more information.
• Transcription factor (TF) ChIP-seq (hg19, GRCh38, mm10): profiles binding sites of transcription factors. Available data types include fold change signal (unreplicated and replicated), unreplicated peaks, and optimal IDR thresholded peaks. See the ChIP-seq computational pipeline overview for more information.
• Histone modification ChIP-seq (hg19, GRCh38, mm10): profiles the locations of methylated, acetylated, or otherwise modified histones. Available data types include unreplicated and replicated fold change signal, unreplicated peaks, and optimal IDR thresholded peaks. See the ChIP-seq computational pipeline overview for more information.
• Repli-seq (hg19): profiles nascent DNA replication. Percentage normalized signal tracks are available.
• RRBS (hg19): profiles DNA methylation. Methylation state at CpG tracks are available.

Acknowledgments

Thanks to the ENCODE Consortium, the ENCODE production laboratories, and the ENCODE Data Coordination Center for generating and processing the datasets used here. The ENCODE accession numbers of the constituent datasets are available from the peak details page. Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI, at the ENCODE Data Analysis Center (ZLab at UMass Medical Center) developed this trackhub. Special thanks to Kate Rosenbloom and Jim Kent at UCSC for guidance developing this trackhub.

References

ENCODE Project Consortium, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Charles B. Epstein, Noam Shoresh, Jessika Adrian, et al. 2020. "Expanded Encyclopaedias of DNA Elements in the Human and Mouse Genomes." Nature 583 (7818): 699–710.

Contact

Please contact henry.pratt@umassmed.edu with any questions or comments about this trackhub.