Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

Nucleic Acids Res. 2017 Jan 4;45(D1):D658-D662. doi: 10.1093/nar/gkw983. Epub 2016 Oct 26.


Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and gene regulation. Although rapidly accumulating publicly available ChIP-seq, DNase-seq and ATAC-seq data are a valuable resource for the systematic investigation of gene regulation processes, a lack of standardized curation, quality control and analysis procedures have hindered extensive reuse of these data. To overcome this challenge, we built the Cistrome database, a collection of ChIP-seq and chromatin accessibility data (DNase-seq and ATAC-seq) published before January 1, 2016, including 13 366 human and 9953 mouse samples. All the data have been carefully curated and processed with a streamlined analysis pipeline and evaluated with comprehensive quality control metrics. We have also created a user-friendly web server for data query, exploration and visualization. The resulting Cistrome DB (Cistrome Data Browser), available online at, is expected to become a valuable resource for transcriptional and epigenetic regulation studies.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin Assembly and Disassembly*
  • Chromatin Immunoprecipitation*
  • Databases, Genetic*
  • Epigenesis, Genetic
  • Epigenomics / methods
  • Gene Expression Regulation
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Mice
  • Web Browser*