[Genome] help with ChIP signal mapping

[Rachel Harte]

Hello Elisabeth,
Thank you for your compliment. We do have a number of ENCODE tracks that
involve ChIP-chip data for histone modifications. You can reach the ENCODE
data through the ENCODE portal:
http://genome.ucsc.edu/ENCODE/

The ChIP-chip data is in the ENCODE Chromatin Immunoprecipitation group
whose track controls are to be found below the Genome Browser image.
The Affy ChIP-chip, LI ChIP, LI gIF ChIP, LI Ng, Sanger ChIp, Uppsala and
Yale data all have ChIP-chip data for histone modifications. They may
differ in the cell lines and treatments used so please read the track
descriptions. These may be found by clicking on the track name links
above the track controls.

The ENCODE data status page may be helpful to you too. It summarises a
list of ENCODE tracks that have been released to our public browser site
(Released section) as well as those under development. It also lists the
cell lines used for the experiments used to create the datasets where
applicable. Here is the link to the status page:
http://genome.ucsc.edu/ENCODE/trackStatus.html

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Thu, 17 May 2007, Elisabeth Martinez wrote:

> Hi,
> I am relatively new to ucsc genome browser. I see that under Group in Table browser, there are ENCODE options that have Chromatin IP info, presumably mapping sites of histone modifications across the genome. I need exactly that. I have a list of genes that are up or down regulated by stimuli and I would like to know if there are common modifications they share. What is the best way of doing this type of analysis and what are the various datasets available to double check results, etc?
> This is an excellent resource.
> Thanks so much,
> Elisabeth
>
>
> Elisabeth D. Martinez, Ph.D.
> Instructor
> Department of Pharmacology
> Hamon Center for Therapeutic Oncology Research
> UT Southwestern Medical Center at Dallas
> 6000 Harry Hines Blvd. NB8.114
> Dallas, TX 75390-8593
> elisabeth.martinez at utsouthwestern.edu
> tel: 214-648-5150
> fax: 214-645-5969
>
>
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