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.

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.

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.

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ENCODE data are now available for the entire human genome. All ENCODE data are free and available for immediate use via : Search for displayable tracks and downloadable files Download of data files Visualization in the UCSC Genome Browser (ENCODE data marked with the NHGRI logo) Data mining with the UCSC Table Browser and other UCSC Genome Bioinformatics tools

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. 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.

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.

25 July 2012 - Mouse ENCODE data releases: UW RNA-seq, FSU Repli-chip, CSHL Long RNA-seq (Release 2)

Replication Timing by Repli-chip from ENCODE/FSU: shows genome-wide assessment of DNA replication timing using NimbleGen tiling CGH microarrays. Each experiment represents the relative enrichment of early vs. late S-phase nascent strands in a given cell line, with data represented as a loess-smoothed function of individual timing values at probes spaced at even intervals across the genome. Regions with high values indicate domains of early replication where initiation occurs earlier in S-phase or early in a higher proportion of cells.

RNA-seq from ENCODE/UW: shows RNA-seq measured genome-wide in 25 mouse tissues and cell lines. Poly-A selected mRNA was used as the source for transcriptome profiling of tissues and cell types that also had corresponding DNase I hypersensitive profiles.

Long RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 2): includes a new browser view (Splice Junctions) and 6 new analysis files per experiment (de novo exons, genes and transcripts with expression levels defined by Cufflinks and Flux Capacitor, and expression levels for Ensembl and Cufflinks models at each level).

16 July 2012 - Human ENCODE data releases: CSHL Small RNA-seq (Release 3), UCSC Regulation Transcription Track (Release 2), UW Affy Exon (Release 3), UMass 5C (Release 2)

Small RNA-seq from ENCODE/Cold Spring Harbor Lab (Release 3) : adds 53 additional experiments, with twenty-two new cell lines represented: CD20+, CD34+_Mobilized, HAoAF, HAoEC, HCH, HFDPC, HMEpC, hMSC-AT, hMSC-UC, HOB, HPC-PL, HPIEpC, HSaVEC, HVMF, HWP, IMR90, Monocytes-CD14+, NHDF, NHEM.f_M2, NHEM_M2, SkMC, SK-N-SH. There are also two new variations in protocol (CIP-TAP and untreated) used to create different RNA populations.

UCSC Integrated Regulation: Transcription Levels Assayed by RNA-seq on 9 Cell Lines from ENCODE: includes transcription levels for 2 additional cell lines: HeLa-S3 and HepG2.

Affymetrix Exon Array from ENCODE/University of Washington (Release 3): revokes previously released K562 zinc-finger experiments due to a data merging issue.

Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass. (Release 2): contains reanalyzed peak files and more complete raw data.

02 July 2012 - Quality metrics for human ENCODE data

The ENCODE Consortium analysis working group has analyzed the quality of the data produced using a variety of metrics. The ENCODE portal Quality Metrics page provides spreadsheets showing quality metrics for human ENCODE datasets, along with descriptions of what the metrics are and what they appear to measure. Spreadsheets are provided for DNase-seq, FAIRE-seq, Transcription Factor ChIP-seq, Histone ChIP-seq, and ChIP Controls. This page is linked from the related Data Standards page. Many of the software tools used for quality metrics, along with their citations, can be found on the portal Software Tools page.

26 Jun 2012 - Human ENCODE data releases: GENCODE Genes V12, CSHL Long RNA-seq (Release 2), SYDH Histone (Rel 3), UW DNaseI HS (Rel 5)

Four track updates were released on the hg19 genome browser: Read more.

The sequence and annotation data displayed in the Genome Browser are freely available for academic, nonprofit, and personal use with the following conditions:

• ENCODE data are covered by the ENCODE Consortium Data Release Policy.
• The general Conditions of Use for the UCSC Genome Browser apply.