Cistrome Data Browser and Toolkit: analyzing human and mouse genomic data using compendia of ChIP-seq and chromatin accessibility data

Abstract

The Cistrome Data Browser (DB) at the website (cistrome.org/db) provides about 56,000 published human and mouse ChIP-seq, DNase-seq, and ATAC-seq chromatin profiles, which we have processed using uniform analysis and quality control pipelines. The Cistrome DB Toolkit at the website (dbtoolkit.cistrome.org) was developed to allow users to investigate fundamental questions using this data collection. In this tutorial, we describe how to use the Cistrome DB to search for publicly available chromatin profiles, to assess sample quality, to access peak results, to visualize signal intensities, to explore DNA sequence motifs, and to identify putative target genes. We also describe the use of the Toolkit module to seek the factors most likely to regulate a gene of interest, the factors that bind to a given genomic interval (enhancer, SNP, etc.), and samples that have significant peak overlaps with user-defined peak sets. This tutorial guides biomedical researchers in the use of Cistrome DB resources to rapidly obtain valuable insights into gene regulatory questions

Keywords

ChIP-seq / chromatin accessibility / gene regulatory analysis / transcription factor

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ACKNOWLEDGEMENTS

The authors would like to acknowledge Dr. Zhiping Weng for providing the backup of the Cistrome DB and Dr. Ting Wang for the Wash U Epigenome Gateway Browser. This work is supported by National Institutes of Health of US (U24 CA237617).

COMPLIANCE WITH ETHICS GUIDELINES

The authors Rongbin Zheng, Xin Dong, Changxin Wan, Xiaoying Shi, Xiaoyan Zhang and Clifford A. Meyer declare that they have no conflict of interests.ƒThe article does not contain any human or animal subjects performed by any of the authors.

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