Question for using WGBS data in ENCODE

[JONGHUN LEE]

Hi, I am a student reserching human DNA methylation.

I appreciate for your effort for producing and sharing the WGBS dataset.

Now I am using the public WGBS data of h1-hESC(GSM1002649) and gm12878 (GSM1002650) and I would like to know the bisulfite conversion rate of the two dataset. If there are any information about  it, please let me know.

Thank you.

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JONGHUN LEE
81-80-4735-7565
Department of Medical Genome Science
University of Tokyo

[Brian Lee]

Dear Jonghun Lee,

Thank you for using the UCSC Genome Browser and your question about Whole Genome Bisulfite Sequencing (WGBS) data from ENCODE.

This data was not released to the public UCSC Genome Browser site, due to the complexity of perfecting alignment methods, but is available at GEO and also at the current ENCODE Portal:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1002650
https://www.encodeproject.org/experiments/ENCSR000AJI/

On the ENCODE portal you will find a "General protocol" Track Description document which states these data were produced by the Dr. Richard Myers Lab at the HudsonAlpha Institute for Biotechnology and lists Dr. Florencia Pauli, fpauli at hudsonalpha.org, as the contact for this data.

Please send any data questions about the track to the source laboratory.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

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