Hello Rebecca,
Although the NHGRI ENCODE web portal indicates that
pathway activation by mitogens was a criterion for
selection of the GM06990 cell line, in fact, no
such experiments were submitted to us during the pilot phase
of ENCODE. We concluded this from review of the
submitted ENCODE data and NHGRI confirms this.
We do have ENCODE pilot data for experiments performed on
a variety of other cell lines that were stimulated with various
treatments, including:
* actinomycin-D treated ME-180 cells
* retinoic acid treated HL-60 cells
* interferon-gamma treated HeLa cells
* TNF-alpha treated HeLa cells
Hope this helps,
Kate
------------------------------------
Kate Rosenbloom
ENCODE DCC Technical Project Manager
UCSC Genome Bioinformatics
Rebecca R. Pickin wrote:
> To whom this concerns,
>
> I have been reviewing information about the selected cell types for both the
> ENCODE project and its pilot project. On the page for the pilot project, in
> reference to the selection of the GM06990 cells, it reads
>
> "2. GM06990, an Epstein-Barr virus-transformed B-lymphocyte from the Utah
> CEPH collection was chosen as a representative lymphoblastoid cell line.
> These cells have a normal karyotype and can be stimulated with mitogens to
> activate signal transduction pathways that involve the activation of well
> studied genes in the ENCODE target regions. More information on the
> properties and the use of this cell line is available at Coriell Cell
> Repositories [locus.umdnj.edu]. "
>
> I recognize that this is not on the UCSC site, but I am hoping you might be
> able to help, regardless. My question is, what mitogens are being referred
> to, here (This information was not found on the Coriell website)? Also, is
> there a place where I could find out which submitters used stimulated or
> unstimulated GM06990 cell lines without going through each submission
> individually?
>
> Thank you very much,
>
> Rebecca Roche Pickin, PhD
> Postdoctoral Research Associate
>
> University of Virginia
> Department of Biochemistry and Molecular Genetics
> Jordan Hall Box 800733
> Charlottesville, VA 22908
>
> E-mail: [EMAIL PROTECTED]
> Lab phone: 434.924.2370
> _______________________________________________
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