ENCODE Project at NHGRI    Encyclopedia of DNA Elements

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Experiment Matrix
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  About ENCODE Data

The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

Click to enlarge ENCODE data are now available for the entire human genome. All ENCODE data are free and available for immediate use via :

To search for ENCODE data related to your area of interest and set up a browser view, use the UCSC Experiment Matrix or Track Search tool (Advanced features). The Experiment List (Human) and Experiment List (Mouse) links provide comprehensive listings of ENCODE data that is released or in preparation.

All ENCODE data is freely available for download and analysis. However, before publishing research that uses ENCODE data, please read the ENCODE Data Release Policy, which places some restrictions on publication use of data for nine months following data release.    Read more about ENCODE data at UCSC.


12 Sept 2013 - New UDR ENCODE Download Method Available

The UCSC Genome Browser is pleased to offer a new download protocol to use when downloading large sets of files from our download servers: UDR (UDT Enabled Rsync). UDR utilizes rsync as the transport mechanism, but sends the data over the UDT protocol, which enables huge amounts of data to be downloaded more efficiently over long distances. Read more.

25 July 2013 - BLUEPRINT Epigenome Data Hub and Quick Reference PDF Now Available

We are pleased to announce the addition of the BLUEPRINT Epigenomics Data Hub on the UCSC Genome Browser through our Public Hubs function. All data were produced and processed by the European BLUEPRINT Epigenome project, aimed to generate 100 reference epigenomes from distinct types of haematopoietic cells and their malignant leukaemic counterparts. Please send any data related questions to blueprint-info@ebi.ac.uk. The BLUEPRINT Hub currently contains 8 DNase-seq, 48 DNA methylation, 170 Histone modification, and 24 RNA-seq tracks, focused on displaying variation in human monocyte and neutrophil cells from 7 adult blood and 4 cord blood samples. Future releases of data for additional samples are planned at a regular basis.

Also the ENCODE Quick Reference Card is now available in PDF courtesy of OpenHelix on the ENCODE Education and Outreach page.

28 May 2013 - ENCODE portal changes: New Link to NHGRI Tutorials, New External Software Tools Page, Updates to Publications including New 2013 Consortium Papers Section

The ENCODE portal was updated to include informative new and expanded pages. A new link to the NHGRI ENCODE Tutorials was added to the ENCODE Education and Outreach page. A new External Software Tools page was added to expand the existing ENCODE Software Tools resources page. The Publications page was expanded to include a new 2013 Consortium-funded section and updated with several new references as well as the non-ENCODE Publications page. Lastly other pages were updated with new information including the ENCODE Analysis Software page, and Quality Metrics page.

13 May 2013 - Uniform Peaks of Transcription Factor ChIP-seq from ENCODE/Analysis

UCSC has released a new browser track containing 690 datasets of transcription factor ChIP-seq peaks based on data from all five ENCODE TFBS ChIP-seq production groups from the project inception in 2007 through the ENCODE March 2012 data freeze. The track covers 161 unique regulatory factors (generic and sequence-specific factors), spanning 91 human cell types, some under various treatment conditions.

Browser track: Transcription Factor ChIP-seq Uniform Uniform Peaks from ENCODE/Analysis
File downloads: Directory File selection tool

This track represents peak calls (regions of enrichment) generated by the ENCODE Analysis Working Group (AWG) using the uniform processing pipeline developed for the ENCODE Integrative Analysis effort and published in a set of coordinated papers in September 2012. Peak calls from that effort (based on datasets from the January 2011 ENCODE data freeze) are available at the ENCODE Analysis Data Hub. The new Uniform TFBS track at UCSC includes newer data, slightly modified processing methods, and improved metadata. Quality metrics are included in metadata, with detailed metrics in a quality spreadsheet linked to the track description. Browser users will see the uniform peaks first when using track search for TFBS, and this track is now the default track shown when the ENCODE TF Binding menu item is selected in the browser.

The primary and lab-processed data (along with methods descriptions, credits and references) on which this track is based are available in the following ENCODE tracks: HAIB TFBS, SYDH TFBS, UChicago TFBS, UTA TFBS, UW CTCF Binding. Many thanks to Anshul Kundaje of the ENCODE AWG for providing the uniform peaks data, description, and quality spreadsheets.

7 April 2013 - User Resources and Frequently Asked Questions page added to website

This new page provides links to ENCODE informational material and tools at the NHGRI, GEO, UCSC, and Nature, together with links to some of the most useful pages at encodeproject.org. It also includes a helpful FAQ section culled from ENCODE questions received on the ENCODE and Genome Browser mailing lists.

  Conditions of Use

The sequence and annotation data displayed in the Genome Browser are freely available for academic, nonprofit, and personal use with the following conditions: