ENCODE Project at NHGRI    Encyclopedia of DNA Elements
Human

Data Summary
Search
Downloads
Genome Browser (hg18)
Genome Browser (hg19)
Preview Browser (hg19)
Session Gallery
Cell Types

Mouse

Data Summary
Search
Downloads
Genome Browser (mm9)
Preview Browser (mm9)
Cell Types

General

Registered Variables
Antibodies
Release Log
Data Policy
Data Standards
Contributors
Publications
Pilot Project
Jobs
Contact Us

  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 Track Search tool (Advanced features). The Data Summary shows a comprehensive listing of ENCODE data that is released or in preparation. Early access to pre-release ENCODE data is provided at http://genome-preview.ucsc.edu. If you would like to receive notifications of ENCODE data releases and related news by email, subscribe to the encode-announce mailing list. For more information about how to access this data, see the free online OpenHelix ENCODE tutorial.

To complement the human ENCODE data, Mouse ENCODE experiments are currently underway. Early access to this data is available on the Mouse mm9/NCBI37 browser at the UCSC preview site. The Mouse ENCODE Data Summary lists experiments that are planned or in progress.

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.




  News  




22 April 2011 - ENCODE data releases: UTA TFBS, UW CTCF, UNC FAIRE, RIKEN CAGE Loc, UW Affy Exon, UW DNaseI DGF & Duke DNaseI HS

Seven tracks of ENCODE data on the GRCh37/hg19 human assembly were released in March and April from the University of Texas at Austin (Open Chromatin), University of Washington, University of North Carolina (Open Chromatin), RIKEN, and Duke University (Open Chromatin) ENCODE groups (6 of the tracks are new to hg19, and one is a Release 2 on hg19):

UTA TFBS: This track displays chromatin immunoprecipitation (ChIP-seq) evidence as part of the four Open Chromatin track sets.

UW CTCF: This track displays maps of genome-wide binding of the CTCF transcription factor in different cell lines using ChIP-seq high-throughput sequencing.

UNC FAIRE: This track displays Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) evidence as part of the four Open Chromatin track sets.

RIKEN CAGE Loc: This track shows 5' cap analysis gene expression (CAGE) tags and clusters in RNA extracts from different sub-cellular localizations in multiple cell lines.

UW Affy Exon: This track displays human tissue microarray data using Affymetrix Human Exon 1.0 GeneChip.

UW DNaseI DGF (Release 2): This track contains deep sequencing DNase data that will be used to identify sites where regulatory factors bind to the genome (footprints).

Duke DNaseI HS: This track displays DNaseI hypersensitivity (HS) evidence as part of the four Open Chromatin track sets.


14 February 2011 - ENCODE data releases: Caltech RNA-seq, Broad Histone, UW Histone & SUNY RIP Tiling. Four tracks of ENCODE data on the GRCh37/hg19 human assembly from the Caltech, Broad/MGH, SUNY Albany and University of Washington ENCODE groups were released. Read more.


9 February 2011 - First Mouse ENCODE data release: Transcription Factor Binding Sites by ChIP-seq from Stanford/Yale The first Mouse ENCODE data is now available on the mm9 (NCBI37) genome assembly. Read more.




  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: