Friday, January 17, 2014

Getting information about ENCODE dataset

The ENCODE project has vast amounts of interesting data to offer. However for me it was not very clear how to get detailed information about a particular sample. Here is a quick short-cut.

I was searching for raw RNA-seq data from several cancer cell-lines.
There is a a web-interface that allows to search inside ENCODE datasets by applying particular filters. In my case I used filters "Cell, tissue or DNA sample" and "Experiment type".

The result of the query is a list of files describing samples, which pass the search criteria. Most likely one might be willing to get more information about a particular sample. However, in the table describing the results I could not find a link to a corresponding publication or at least to a page with the description of the dataset.

One way to find this information is to copy the GEO sample accession and then search for it in the GEO Accession viewer.

From GEO-sample there is usually a link to the GEO-series which has also the link to the publication.

Note, that if you are searching for tracks, it is easy to obtain summary of the track just by double clicking on it after adding in the UCSC Genome browser.

Hope that was useful!

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