[Genome] Jurkat Cell line Expressions

[Rachel Harte]

David,

Sp1 and Sp3 are transcription factors whose binding sites were identified
in the ChIP/chip experiments. The ChIP/chip method is used to
identify DNA regions/promoters to which these factors are bound. The Sp1 or
Sp3 was crosslinked to the DNA in Jurkat cells. The DNA was extracted and
then sheared to produce fragments with an average size of 500 bp. Then
the this was immunoprecipitated with an antibody against Sp1 or Sp3. Bound
immune complexes were recovered, cross-links were reversed and the bound DNA
was extracted. This DNA was then hybridised to a tiling array (consisting
of probes tiled across the genome) to determine which region of the genome is
binding this transcription factor in the Jurkat cell line under the
experimental conditions used.

To find out more about the tracks relating to the tables that you found, go
to the Genome Browser through the ENCODE portal for hg17:
http://genome.ucsc.edu/ENCODE/encode.hg17.html

then scroll down to the ENCODE Chromatin Immunoprecipitation group and
click onthe Stanf ChIP link above the track control there is a description
of the data and a link to the paper describing the methods used.
Similarly, there is a description for the Stanf ChIP Score. The
encodeStanfordChipJurkatSp1 and encodeStanfordChipJurkatSp3 tables are
from the Stanf ChIP track (Stanford ChIP/chip (Jurkat cells, Sp1 ChIP) and
Stanford ChIP/chip (Jurkat cells, Sp3 ChIP) subtracks respectively). The
encodeStanfordChipSmoothedJurkatSp1 and
encodeStanfordChipSmoothedJurkatSp3 tables are from the Stanf ChIP Score
track (Stanford ChIP/chip Smoothed Score (Jurkat cells, Sp1 ChIP) and
Stanford ChIP/chip Smoothed Score (Jurkat cells, Sp3 ChIP) subtracks
respectively).

The description of the Methods for these two tracks describes how they
differ. The raw data is in the Stanf ChIP track while the Stanf ChIP Score
track has scores created for visualisation purposes only. For any analysis,
the Stanf ChIP track data should be used.

If you go to our downloads server, you can download the data for these
tables. The downloads server is at:

http://hgdownload.cse.ucsc.edu/

If you click on Human and then scroll to the hg17 assembly and click on
the Annotation database link, you will find a database dump of all the
tables for hg17. You will can download these tables here. For the
Stanf ChIP track data, the regions in the tables represent the regions of
the genome (probes from the tiling array) which were hybridized to
the DNA that was bound by the transcription factor. The score is the
normalized and transformed mean ratio of ChIP DNA:Total DNA calculated
from the array data.

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 Mon, 30 Apr 2007, David L Klinkebiel wrote:

> Rachel,
>
> I found the files:
> encodeStanfordChipJurkatSp1
> encodeStanfordChipJurkatSp3
> encodeStanfordChipSmoothedJurkatSp1
> encodeStanfordChipSmoothedJurkatSp3
>
> These files seem to have chromosome locations with a value.  What is the
> value as far as expression and what is the difference between Sp1 and Sp3
> and ChipJurkat and ChipSmoothed. Thank you.
>
> David Klinkebiel, Ph.D.
> Department of Biochemistry and Molecular Biology
> University of Nebraska Medical Center
> 985870 Nebraska Medical Center
> Omaha, NE 68198-5870
> Office Phone: 402-559-3842
> Lab Phone: 402-559-9303
> FAX: 402-559-6650
>
> ***The University of Nebraska Medical Center E-Mail Confidentiality
> Disclaimer***
> The information in this e-mail may be privileged and confidential, intended
> only for the use of the addressee(s) above.
> Any unauthorized use or disclosure of this information is prohibited. If you
> have received this email by mistake,
> please delete and immediately contact the sender.
>
> -----Rachel Harte <hartera at soe.ucsc.edu> wrote: -----
>
>       To: dklinkebiel at unmc.edu
>       From: Rachel Harte <hartera at soe.ucsc.edu>
>       Date: 04/27/2007 06:42PM
>       Subject: Re: [Genome] Jurkat Cell line Expressions
>
>       David,
>       We have some Jurkat cell line expression data in the hg17
>       ENCODE Stanford
>       ChIP/chip tracks (Stanf ChIP and Stanf ChIP Smooth). These
>       are both in the
>       ENCODE Chromatin Immunoprecipitation tracks group. Is this
>       the data that
>       you are referring to? Please clarify what you are looking
>       for.
>       Thanks.
>
>       Rachel
>
>       Rachel Harte
>       UCSC Genome Bioinformatics Group
>       http://genome.ucsc.edu
>
>       > Subject:
>       > Jurkat Cell line Expressions
>       > From:
>       > David L Klinkebiel <dklinkebiel at unmc.edu>
>       > Date:
>       > Thu, 26 Apr 2007 17:53:59 -0500
>       > To:
>       > genome at soe.ucsc.edu
>       >
>       > To:
>       > genome at soe.ucsc.edu
>       >
>       >
>       > I was wondering if it would be possible to get the complete
>       database of
>       > Jurkat Cell Line Expression values for all the available
>       genes in value
>       > form. Thank you.
>       >
>       >
>       > David Klinkebiel, Ph.D.
>       > Department of Biochemistry and Molecular Biology
>       > University of Nebraska Medical Center
>       > 985870 Nebraska Medical Center
>       > Omaha, NE 68198-5870
>       > Office Phone: 402-559-3842
>       > Lab Phone: 402-559-9303
>       > FAX: 402-559-6650
>       >
>       > ***The University of Nebraska Medical Center E-Mail
>       Confidentiality
>       > Disclaimer***
>       > The information in this e-mail may be privileged and
>       confidential, intended
>       > only for the use of the addressee(s) above.
>       > Any unauthorized use or disclosure of this information is
>       prohibited. If you
>       > have received this email by mistake,
>       > please delete and immediately contact the sender.
>
>
>
>