More mouse ENCODE data is flowing out!

Good news–more of the mouse data that I promised in the ENCODE training materials is really coming along now!  When we first did the materials with the folks at UCSC who are sponsoring the free access to the ENCODE tutorial, I had a piece that said mouse data was going be coming. There was an announcement a few months back that offered the first stuff–some mouse TFBS (transcription factor binding site) data, but now that data is really flowing out. Just from the ENCODE mailing list the other day, this announcement:

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The ENCODE Data Coordination Center at UCSC is pleased to announce the release of the following new tracks on the mm9 genome browser based on data from the UCSD/Ludwig Institute for Cancer Research, University of Washington, and Stanford/Yale Mouse ENCODE groups.

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Histone Modifications by ChIP-seq from ENCODE/LICR

This track shows a comprehensive survey of cis-regulatory elements in the mouse genome by using ChIP-seq to identify transcription factor binding sites and chromatin modification profiles in many mouse tissues and primary cells, including bone marrow, cerebellum, cortex, heart, kidney, liver, lung, spleen, mouse embryonic fibroblast cells (MEFs) and embryonic stem (ES) cells.

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeLicrHistone

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DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington

This track shows DNaseI sensitivity measured genome-wide in mouse tissues and cell lines using the Digital DNaseI methodology and DNaseI hypersensitive sites. DNaseI has long been used to map general chromatin accessibility and DNaseI hypersensitivity is a universal feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include enhancers, insulators, promotors, locus control regions and novel elements.

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeUwDnase

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Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale

This track shows probable locations of the specified histone modifications in B-cell lymphoma (CH2) and Leukemia (MEL) cells as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq).

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeSydhHist

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Thanks to all who had a hand in generating this data, and the UCSC wranglers and Q/A staff who made these data releases possible.

The list of all released ENCODE data is available from the ‘Release Log’ link at the ENCODE DCC web portal: http://genome.ucsc.edu/ENCODE/releaseLog.html

For questions about a specific ENCODE track, click the ‘Contact’ link listed on the track description page. For general questions about ENCODE data at UCSC, contact the ENCODE DCC team at: [email on this page].

Katrina Learned

ENCODE DCC QA Team Lead

UCSC Genome Bioinformatics Group

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Check it out! If you want some guidance on the overall structure of the ENCODE project and how the data is organized at UCSC, check out the tutorial:  http://openhelix.com/ENCODE

Go directly to the ENCODE portal at UCSC with this link: http://encodeproject.org/ENCODE/