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 the consortium is to build a comprehensive parts list of the functional elements of the human genome, including elements that act at the protein level (coding genes) and RNA level (non-coding genes), and regulatory elements that control the cells and circumstances in which a gene is active. The discovery and annotation of gene elements is accomplished primarily by sequencing RNA from a diverse range of sources, comparative genomics, integrative bioinformatic methods, and human curation. Regulatory elements are typically investigated through DNA hypersensitivity assays, assays of DNA methylation, and chromatin immunoprecipitation (ChIP) of proteins that interact with DNA, including modified histones and transcription factors, followed by sequencing (ChIP-Seq). The results of ENCODE experiments, collected in the ENCODE DCC database, are displayed on the UCSC Genome Browser. The data can also be downloaded from the ENCODE DCC website in text format.

To access ENCODE data, open the Genome Browser, select the March 2006 assembly of the human genome, and go to your region of interest. ENCODE tracks will be marked with the NHGRI logo . The bulk of the ENCODE data can be found in the Expression and Regulation track groups, with a few in the Mapping, Genes, and Variation groups. Although most participating research groups have provided several tracks, generally only selected data from each research group are displayed by default. Click the hyperlinked name of a particular track to display a page containing configuration options and details about the methods used to generate the data. See the Genome Browser User's Guide for further information about displaying tracks and navigating in the Genome Browser. To receive notifications of ENCODE data releases and related news by email, subscribe to the encode-announce mailing list.

Data from the earlier pilot phase of the ENCODE project are available on the May 2004 and March 2006 human assemblies. These datasets are generally available only in the initial ENCODE-targeted regions that covered approximately 1% of the genome. The ENCODE Pilot Project web pages provide convenient browser access to these regions.

Before publishing research that uses ENCODE data, please read the data release policy, which places some restrictions on publication use of data for nine months following the data release.

Sep 2009 data freeze complete:  The ENCODE Consortium has just completed data submissions for the fourth production data freeze (Sep 09). The first set of data from this freeze to complete quality review is now available on the UCSC public server, in Release 2 of the ENCODE Transcription Factor Binding Sites from Yale/UC-Davis/Harvard track. Release 2 adds 59 ChIP-seq experiments to this track.

Other October track releases:  The Affymetrix/CSHL Subcellular RNA Localization by Tiling Array track was expanded to include 4 additional experiments.

encodeproject.org:  By request of the ENCODE Consortium, the domain encodeproject.org has been registered by the ENCODE Data Coordination Center, and is redirected to the ENCODE portal at UCSC.

New grants funded:  NHGRI has funded 5 new ENCODE grants, as part of the American Investment and Recovery Act. The new grants include expansion of ENCODE to the mouse genome and proteogenomics.

Job openings at UCSC:  The UCSC Genome Browser and ENCODE projects are currently accepting applications for Software Developer and Biological Database Testing/User Support Technician positions. We are looking for talented individuals who would like to use their skills in computer science, biology, and bioinformatics on fast-paced projects featuring the work of top genomics scientists worldwide.

During this period a total of 10 new ENCODE tracks were released to the UCSC public server. Functional elements and region characterization in these tracks include:

• DNaseI hypersensitive sites and hotspots (University of Washington)
• Regions of DNA methylation, by Methyl-seq and Illumina 27 array (HudsonAlpha Institute)
• Bi-directional promoters and negative regulatory elements (NHGRI Elnitski lab)
• Transcriptome profiling by RNA-seq, including single-molecule sequencing (CSHL, Helicos)
• Expression levels by exon array (University of Washington)
• Regions of copy number variation (HudsonAlpha Institute)
• Mappability/uniqueness of nmers (University of Massachusetts, Duke, Broad, Rosetta)

For track names and file access, see the Release Log and Downloads links listed in the left menu bar.

We would like to thank the contributing ENCODE labs and the the DCC team at UCSC for their efforts completing these tracks.

During this period, a total of seven new ENCODE tracks were released to the UCSC public server. These tracks include high-quality gene annotations, maps of transcription factor binding, histone modifications, and open chromatin, RNA subcellular localization, and RNA/protein binding sites. 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 is covered by the ENCODE Consortium Data Release Policy.
• The general Conditions of Use for the UCSC Genome Browser apply.