UCSC Preview Browser server, and Mouse TFBS data

Hey folks–here’s a couple of hot updates from the UCSC ENCODE team, via the ENCODE announcement mailing list. First, they are announcing access to their preview server.

For a long time it’s been possible to access the test server, but this is a new way to access a weekly mirror of everything that’s on their internal development server.  I’m going to just give you Kate’s whole announcement here, for the full story:

Early access to ENCODE and other UCSC browser data tracks under construction is now available from the new UCSC Preview Browser site:

http://genome-preview.ucsc.edu

This site is a weekly mirror of our internal development server for public access. Data and tools there 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://genome.ucsc.edu.

Cheers,

Kate

So keep in mind that it’s possibly a little variable what you’ll see–but early access to the new data is very cool.

There was also a separate announcement from the ENCODE team that the first mouse Transcription Factor Binding Site (TFBS) data has just come along. I mentioned that at our workshop at USC last week, but unless you were monitoring the downloads page you might not have see that notice. Very cool. The human data that’s been on there for a while now is very popular with all the folks we show it to in our workshops–and there are a lot of transcription factors represented in the human data set right now.

The ENCODE Data Coordination Center at UCSC is pleased to announce the release of the first production Mouse ENCODE data. These data have been released on the NCBI37/mm9 mouse assembly and are from the Stanford/Yale Mouse ENCODE group:

Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale

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This track shows probable binding sites of the following transcription factors, c-MYB (H-141), CTCF (C-20), Max, NELFE, p300 (N-15), Rad21, and USF2, in the Leukemia (K562 analog) cell line as determined by chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq).

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

http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/

Thanks to all who had a hand in generating this data and to the UCSC wrangler, Venkat Malladi, and Q/A staff who made this data release 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: encode@soe.ucsc.edu.

Katrina

If you aren’t familiar with the ENCODE project, the data, and how to find in the UCSC Genome Browser you should check out the tutorial. It’s freely available, sponsored by the UCSC team:

http://openhelix.com/ENCODE