Data Release from ENCODE: 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. View the participants and projects in this phase of ENCODE.

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).

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. View the new data release policy.