Encyclopedia of DNA Elements
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About ENCODE Data
| 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.
Click to enlarge | 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 Track Search tool (Advanced features). The Data Summary shows a comprehensive listing 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. To complement the human ENCODE data, Mouse ENCODE experiments are currently underway. Early access to this data is available on the Mouse mm9/NCBI37 browser at the UCSC preview site. The Mouse ENCODE Data Summary lists experiments that are planned or in progress. 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. |
News |  |
| 29 Oct 2011 - Human ENCODE data releases: SYDH TFBS, CSHL Long RNA-seq, GIS RNA PET, UW DNaseI HS (release 3), Mapability (Release 3) Three new tracks and two track updates were released on the hg19 genome browser: ENCODE Transcription Factor Binding Sites by ChIP-seq from Stanford/Yale/USC/Harvard: This comprehensive track shows 306 ChIP-seq experiments identifying transcription factor binding sites in 19 cell types. Long RNA-seq from ENCODE/Cold Spring Harbor Lab: This comprehensive track from the ENCODE Transcriptome group shows RNAs longer than 200 nucleotides. Profiling was performed on RNA extracts enriched and depleted for polyA+, in multiple cellular compartments and whole cell, in 15 cell lines. RNA Subcellular Localization by Paired End diTag Sequencing from GIS/ENCODE: This track from the ENCODE Transcriptome group shows starts and ends of full length mRNA transcripts determined by GIS paired-end ditag (PET) sequencing. Experiments were conducted in 7 cell lines and one tissue (prostate), with RNA extracted from 6 isolated cellular compartments and in whole cell. 19 Sept 2011 - Mouse ENCODE data releases: Stan/Yale Histone, LICR TFBS, LICR RNA-seq, Stan/Yale TFBS (Release 2) Three new tracks and one track update were released on the mm9 genome browser: Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale: This track shows locations of histone H3K4me3 modification in CH12 and MEL cell types. The two cell lines were selected for similarity to the ENCODE Tier1 cell lines (GM12878 and K562). Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR, and RNA-seq from ENCODE/LICR: These tracks show transcriptome and Pol2, p300 and CTCF binding sites in mouse bone marrow, cerebellum, cortex, heart, kidney, liver, lung, spleen, embryonic fibroblast cells (MEFs) and embryonic stem (ES) cells. Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale (Release 2): This release adds binding site localization for 13 additional transcription factors to the previously released TFBS track. 15 Sept 2011 - Summer ENCODE human data releases: GENCODE Genes V7, HAIB TFBS, Stanf Nucleosome, HAIB Genotype, SUNY RIP-seq, SUNY Switchgear Six tracks of human ENCODE data were released in late summer on the hg19 genome browser: 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: ENCODE data are covered by the ENCODE Consortium Data Release Policy. The general Conditions of Use for the UCSC Genome Browser apply. |