Track -Chromatin Interaction Analysis Paired-End Tags (ChIA-PET) from ENCODE/GIS-Ruan

[Nickolai Tchurikov]

Dear Colleagues,

During the last summer (2013) I used the track ChIA-PET from ENCODE/GIS-Ruan in the
UCSC browser. In the corresponding GEO databases (GSE39495)it is
indicated that "The protein factors displayed in the track include estrogen receptor
alpha (ERa), RNA polymerase II (RNAPII), and CCCTC binding factor (CTCF).".

Does it means that you used the mixture of three antibodies or you
included the separate obtained final data on the same track?

Nickolai.


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Nickolai A. Tchurikov, M.D., Ph.D.,
Department of Epigenetic Mechanisms of Gene Expression Regulation,
Engelhardt Institute of Molecular Biology,
Vavilov Str. 32, 119991 Moscow, Russia
E-mail: tchu...@eimb.ru
Phone: +7-499-135-97-53; Fax: +7-499-135-14-05

[Brian Lee]

Dear Nickolai,

Thank you for using the UCSC Genome Browser and your question about ChIA-PET from ENCODE/GIS-Ruan track data.

By navigating to the track description page for the data you can find a Methods section that explains the procedure used to produce the data:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisChiaPet

If more questions persist after reading the Methods section, under the Credits section you can find a contact to send further inquiries about the data production process.

A quick note, you may find this ENCODE resource page of interest: http://genome.ucsc.edu/ENCODE/FAQ/index.html

There are answers to some frequently asked questions, such as one about loading GEO data, where you can search for accession numbers such as by using the Track Search tool: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hgt_tSearch=1&tsCurTab=simpleTab&tsSimple=GSE39495

Click search, and change results from "hide" to "full" to see the data in the browser. Then click the left hand grey bar to arrive at the Track Configuration page that will be the same above link with the Track Description.

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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