ENCODE Project at NHGRI    ENCODE Data Coordination Center at UCSC
  Home   -   Terms   -   Help  
Genome Browser
Cell Types
Release Log
Downloads
Contributors
Publications
Data Policy
Pilot Project
Contact Us

  About the ENCODE Data Coordination Center (DCC)

The UCSC Genome Browser displays data produced by the Encyclopedia of DNA Elements (ENCODE) Consortium, 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 the functional elements in the human genome.

In September 2007, the ENCODE project was scaled up from a pilot phase to cover the entire human genome. To access genome-wide ENCODE data in the Genome Browser, go to your region of interest and select ENCODE tracks (marked with the NHGRI logo ).

During the pilot phase of the ENCODE project (2003-2007), experiments focused on a limited set of genomic regions comprising roughly 1% of the human genome. Data limited to the pilot regions is located in ENCODE-specific track groups in the browser. The ENCODE Pilot Project web pages provide convenient browser access to these regions.

Other key differences from the pilot project are:
  • Identification of common cell types to facilitate integrative analysis
  • New experimental technologies based on high-throughput sequencing
  • A data release policy restricting use of data for nine months following release

Click here to go to the main UCSC Genome Browser site, which provides access to sequence and annotation data for a large collection of genome assemblies. See the Genome Browser User's Guide for information about displaying tracks and navigating in the Genome Browser.



  News  

13 March 2009 - ENCODE Data Release: Transcription Factor Binding Sites from Yale/UC-Davis/Harvard

We are pleased to announce the release to the ENCODE DCC/UCSC public server of the ENCODE Transcription Factor Binding Sites by ChIP-seq from Yale/UC-Davis/Harvard (Yale TFBS, in the Regulation group). This track shows probable binding sites of 12 transcription factors and RNA polymerase II in 7 cell types, as determined by chromatin immunoprecipitation followed by high-throughput sequencing. The Genome Browser displays discrete Peaks of enrichment and Signal graphs of enrichment density for these experiments. The sequence reads, quality scores, and sequence alignment coordinates from these experiments are available for download.

We would like to acknowledge the efforts of the Yale/UC-Davis/Harvard ENCODE group and the work of the UCSC data wrangler for this group, Tim Dreszer, for completing this track. We also thank the entire UCSC ENCODE team and the UCSC Quality Assurance group for contributing to this first ENCODE track release.


27 Feb 2009 - ENCODE February 2009 data freeze

The February 2009 ENCODE data freeze supplements the data contributed for the November 2008 freeze, and will be used together with the earlier freeze for the initial analysis effort of the ENCODE Consortium. Data from this freeze is being incorporated into tracks created from the first data freeze, and is being reviewed by the UCSC Quality Assurance team.


9 Dec. 2008 - First ENCODE whole-genome data freeze completed

The ENCODE Consortium has just completed the first freeze (November 2008) of whole-genome experimental data produced for the ENCODE production phase. Data submitted to the DCC for this freeze include:

  • transcription factor binding sites
  • histone modifications
  • DNaseI hypersensitive sites
  • DNA methylation
  • transcription maps and tags, localized to subcellular compartments
  • GENCODE gene annotations

Experiments during this freeze focused on the ENCODE Tier1 cell lines -- K562 leukemia, and GM12878 lymphoblastoid (which is also a 1000 Genomes project sample designated for in-depth analysis of genetic variation). The freeze also includes data from some ENCODE Tier2 and Tier3 cell lines (see Cell Types). The majority of these experiments were assayed by high-throughput sequencing (ChIP-seq, DNase-seq, and RNA-seq).

The UCSC quality team is currently reviewing these data. When the review is complete, the browser tracks and associated downloads will be released to the UCSC public Genome Browser.

Thanks to the many labs who contributed data for the initial phase of this project. We'd also like to acknowledge the UCSC ENCODE team for data wrangling during the freeze, and for the development and maintenance of the ENCODE automated data submission pipeline and associated tools: Kate Rosenbloom, Tim Dreszer, Larry Meyer, Michael Pheasant, Ting Wang, Galt Barber, and Andy Pohl.


  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: