ENCODE Question

[Sample, Jeff]

The EBV-transformed B-cell line GM12878 is one of the Tier 1 cell lines being used for analysis. I am interested in EBV-specific data, e.g., RNA-Seq, that may be available from the analyses of this particular cell line. I have not been able to find any reference to EBV data through the UCSC portal, and searches for “EBV” in the FAQ section came up negative.

 

Are there EBV data available from the ENCODE project, and if so, how would I access this?

 

Thank you!

 

Sincerely,   

 

Jeff Sample

 

Jeffery T. Sample, Ph.D.

Professor

Department of Microbiology & Immunology - H107

Penn State University College of Medicine

Penn State Hershey Cancer Institute

500 University Dr.

Hershey, PA 17033-2360

Tel: 717-531-0003 ext 287151

Fax: 717-531-6522

E-mail: jsa...@hmc.psu.edu

 

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[Brian Lee]

Dear Jeff Sample,

Thank you for using the UCSC Genome Browser and your question about accessing data available from the ENCODE project, specifically RNA-seq from the GM12878 Epstein–Barr virus transformed cell line.

On the left hand side from the UCSC portal, if you click "ENCODE" you will arrive to the ENCODE portal, http://genome.ucsc.edu/ENCODE/. From the ENCODE portal you can find a link to human "Cell Types", or click to the link to the "Resources & FAQ page" to find additional information along with the same link, http://genome.ucsc.edu/ENCODE/cellTypes.html. On the Cell Types page you can see "Epstein-Barr Virus" included in the description of the GM12878 cell line. You can review all the other cell lines to see if any other might also be of interest, for example a quick search show GM06990, GM10847, and many others include "Epstein" in their descriptions.

Our File Search and Track Search tools, http://genome.ucsc.edu/ENCODE/search.html, accessible from the ENCODE portal and Resources page, can help you search for all the tracks and files specific to a certain cell line like GM12878.

Click on the "File Search" link for the human hg19 assembly and then on the "Cell, tissue, or DNA sample" menu select GM12878 (you could also select additional cell lines like GM06990...). Clicking search will bring up a total up the first 1000 files of many files for GM12878. For GM12878 you will need to further refine your selection by including other parameters, such as including "Experiment (Assay) type" and selecting "RNA-seq", this will still bring up 334 files you can review and download.

By using Track Search on the hg19 assembly with the same parameters, GM12878 and RNA-seq, you will pull up 102 tracks that you can selectively change the visibility setting on and immediately view on the UCSC Genome Browser.

Lastly, from the ENCODE portal you can access the human downloads page, http://genome.ucsc.edu/ENCODE/downloads.html. Here you can find a link to the track hub for the uniform RNA-seq files and tracks from the ENCODE Analysis Working Group (AWG) based on a uniform processing pipeline that may also be of interest: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=hub_4607_uniformRNA&hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt

Thank you again for your inquiry and using the UCSC Genome Browser. If you have further questions, please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genome Bioinformatics Group

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