ENCODE Project at NHGRI    Encyclopedia of DNA Elements
Human

Data Summary
Search
Downloads
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
Education and Outreach
Release Log
Data Policy
Data Standards
File Formats Publications
Contributors
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.

[an error occurred while processing this directive]

WARNING: This is a test site. Data and tools here are under construction, have not been quality reviewed, and are subject to change at any time. For high-quality reviewed annotations on our production server, visit http://encodeproject.org.

[an error occurred while processing this directive]

WARNING: This is our preview site. This website is a weekly mirror of our internal development server for public access. Data and tools here are under construction, have not been quality reviewed, and are subject to change at any time. We provide this site for early access, with the warning that it is less available and stable than our public site. For high-quality reviewed annotations on our production server, visit http://encodeproject.org.

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  




5 Jan 2012 - Human ENCODE data releases: UW Histone, HAIB Methyl450, RIKEN CAGE Loc, UW Affy Exon (Release 2)

Three new tracks and one track update were released on the hg19 genome browser:

Histone Modifications by ChIP-seq from ENCODE/University of Washington: This track shows genome-wide maps of histone modifications associated with active promoters (H3K4me3), repressed regions (H3K27me3), and active transcription (H3K36me3) in 57 cell types, as identified by ChIP-seq.

CpG Methylation by Methyl 450K Bead Arrays from ENCODE/HAIB: This track displays the methylation status of specific CpG dinucleotides in 61 cell types as identified by the Infinium Human Methylation 450 Bead Array platform. In general, methylation of CpG sites within a promoter causes silencing of the gene associated with that promoter.

RNA Subcellular CAGE Localization from ENCODE/RIKEN: This track from the ENCODE Transcriptome group shows 5' cap analysis gene expression (CAGE) tags and clusters. A total of 34 Experiments were conducted in 12 cell lines and one tissue (prostate), with RNA extracted from 6 isolated cellular compartments and in whole cell.

Affymetrix Exon Array from ENCODE/University of Washington (Release 2): This track from the ENCODE Transcriptome group shows human tissue miroarray data from the Affymetrix Human Exon 1.0 GeneChip. Release 2 of this track shows experiments in 14 additional cell lines.


1 Dec 2011 - Mouse ENCODE data releases: Caltech TFBS, Caltech Histone

Two new tracks were released on the mm9 genome browser:

Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech: This track shows 15 ChIP-seq experiments mapping 7 histone marks in the C2C12 myoblast cell line; both untreated cells and cells under timecourse treament with insulin to stimulate myogenesis.

Histone Modifications by ChIP-seq by ChIP-seq from ENCODE/Caltech: This track shows 26 ChIP-seq experiments mapping 14 transcription factors in the C2C12 myoblast cell line; both untreated cells and cells under timecourse treament with insulin to stimulate myogenesis.


10 Nov 2011 - ENCODE portal changes: New File Formats page and updates to Publications, Data Summaries, and Data Standards

The ENCODE portal was updated to include informative new and expanded pages. ENCODE-related data file formats are now documented on the new File Formats page. The Publications page was expanded to a comprehensive list of Consortium publications, plus methods, resource, and biological findings papers by ENCODE-funded projects. The Human Data Summary and Mouse Data Summary spreadsheets detailing ENCODE submissions were updated to reflect status as of the latest ENCODE quarterly reporting (Sept. 30 2011). Finally, the Data Standards section was greatly expanded to include new standards documents (v2.0 ChIP-seq) and a new Platform Characterization section.


29 Oct 2011 - Human ENCODE data releases: SYDH TFBS, CSHL Long RNA-seq, GIS RNA PET, UW DNaseI HS (release 3), Mapability (Release 3)

Three new tracks and two track updates were released on the hg19 genome browser: 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: