The ENCODE project and the Data Coordination Center at UCSC had generated huge amounts of data and made it publicly available as quickly as possible on the genome browser. So much data that it’s hard to keep up–and I’m on the mailing list and using the UCSC Genome Browser all the time keeping an eye out for data I’m interested in.
One of the more recent innovations to enable you to find the data types you are interested in is The Matrix. First available for human (the ENCODE Experiment Matrix is the official name), it’s now also on the site and accessible for the mouse data that’s flowing in as well.
It’s a really handy way to explore the data by type of experiment, or cell line, and you can just click to either examine the tracks and turn them on in your browser, or you can choose to download the set. Very popular when we presented it in the recent ENCODE trainings we did.
Mouse Experiment Matrix announcement on the mailing list. From the email:
The ENCODE DCC at UCSC is pleased to announce the release of the portal
‘Experiment Matrix’ for Mouse ENCODE data:
The three web pages in this application (Experiment Matrix, Experiment
Summary, ChIP-seq Matrix) provide an up-to-date view of the publicly
available Mouse ENCODE data, along with an interface for selecting
experiments for viewing in the browser or downloading as files for
analysis. Each page has a file/track selector. Clicking an experiment
item produces a search window with resulting files or tracks listed.
The pages are best viewed in FireFox, Chrome, and Safari browsers, and
zoomed out as far as readability on your screen allows.
ENCODE DCC Technical Project Manager
UCSC Genome Bioinformatics
Go. For background on the ENCODE projects, you can see the ENCODE Foundations tutorial we have, which is freely available as it is sponsored by the UCSC ENCODE team. We are in the process of creating a second one with updates that include the Matrix.