Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes.

Data Access

ChIPBase v3.0 does not provide a way to download the source peak file, you may download peak data in ENCODE website.


[1] ENCODE Project Consortium. Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes. Nature. 2020 July 30;583(7818):699-710
[2] ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. PMID: 22955616; PMC: PMC3439153
[3] ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046. PMID: 21526222; PMC: PMC3079585


Thanks to ENCODE team for generating, processing the ChIP-seq peak data and making them available on ENCODE website.

Data Use Policy

External data users may freely download, analyze and publish results based on any ENCODE data without restrictions. This applies to all datasets, regardless of type or size, and includes no grace period for ENCODE data producers, either as individual members or as part of the Consortium. Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. The Consortium will continue to publish the results of its own analysis efforts in independent publications, as described in Citing ENCODE:
1.Cite the Consortium's most recent publications.
2.Acknowledge the ENCODE Consortium and the ENCODE production laboratory(s) generating the particular dataset(s).
3.Reference the ENCODE accession numbers of the datasets (ENCSR...) and files (ENCFF...) used.