ENCODE Project at NHGRI    Encyclopedia of DNA Elements
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  About ENCODE Data at UCSC




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 at UCSC is freely available for download and analysis.   Read more about ENCODE data at UCSC.




  News  




17 July 2014 - First Data Release from ENCODE Phase 3: 760 experiments of ChIP-seq, RNA-seq, ChIA-Pet and 3 new assay types in human and mouse

The ENCODE Data Coordination Center is pleased to announce the first public release of data from the third phase of ENCODE. This phase represents a continuation of ENCODE and Mouse ENCODE through an additional four years of high-throughput whole-genome data production, with additional resources and emphasis on uniform data processing, analysis and functional validation. The participants and projects in this phase of ENCODE are listed here.

This data release includes the following datasets:

  • Human: 257 ChIP-seq, 164 RNA-seq (includes 25 with shRNA knockdown), 22 RAMPAGE, 7 ChIA-PET, 20 RNA Bind-n-Seq
  • Mouse: 260 ChIP-seq, 2 RNA-seq, 28 Shotgun Bisulfite-seq (WGBS)
New assays in this phase of ENCODE include:
  • RAMPAGE: Identifies transcriptional start sites with quantification (PMID: 24510412, PMID: 22936248)
  • Shotgun Bisulfite-seq (WGBS): Analyzes DNA methylation at high resolution (PMID: 19829295)
  • RNA Bind-n-Seq: Identifies binding sequences and measures affinity of protein binding to RNA, using a cell-free system (PMID: 24837674)
This data, along with all files from the previous phase of ENCODE, are available from the new ENCODE DCC website (encodedcc.org). Use this link to view the new experiments: ENCODE3 Data Releases

Going forward, the DCC website and ENCODE portal will merge to provide a single site with comprehensive information about the ENCODE project and extensive user tools for locating data of interest from all phases of ENCODE production. The ENCODE tools, tracks, and downloads developed during the first production phase will remain available at the UCSC Genome Browser site, http://genome.ucsc.edu/ENCODE. For newer data, the 'Visualize Data' button under the Files section of the new site's Experiment pages launches a Genome Browser view for processed data suitable for visualization.

The new data is released under a rapid release policy by which primary data (e.g. fastq sequence files) are released immediately after validation to data formatting standards. Processed data from these experiments will be released after quality assessment and uniform processing are complete. Unlike the previous ENCODE production phase, there is no moratorium on external use for this data. The new data release policy is available here.


17 April 2014 - New Motif Displays for Transcription Factor ChIP-seq Track and New Genome Segmentations from ENCODE

The latest Transcription Factor ChIP-seq track has been enhanced with the display of Factorbook motifs. 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: