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