Stanf ChIP Track Settings
 
Stanford ChIP-chip (HCT116, Jurkat, K562 cells; Sp1, Sp3 ChIP)   (Stanf ChIP)

This track is part of a parent called 'Stanf ChIP'. To show other tracks of this parent, go to the Stanf ChIP configuration page.

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dense
 Stan HCT116 Sp1  Stanford ChIP-chip (HCT116 cells, Sp1 ChIP)   schema 
dense
 Stan HCT116 Sp3  Stanford ChIP-chip (HCT116 cells, Sp3 ChIP)   schema 
dense
 Stan Jurkat Sp1  Stanford ChIP-chip (Jurkat cells, Sp1 ChIP)   schema 
dense
 Stan Jurkat Sp3  Stanford ChIP-chip (Jurkat cells, Sp3 ChIP)   schema 
dense
 Stan K562 Sp1  Stanford ChIP-chip (K562 cells, Sp1 ChIP)   schema 
dense
 Stan K562 Sp3  Stanford ChIP-chip (K562 cells, Sp3 ChIP)   schema 
    
Data version: ENCODE June 2005 Freeze
Data coordinates converted via liftOver from: July 2003 (NCBI34/hg16)

Description

This track displays regions bound by Sp1 and Sp3, in the following three cell lines, assayed by ChIP and microarray hybridization:

Cell LineClassificationIsolated From
HCT 116colorectal carcinomacolon
Jurkat, Clone E6-1acute T cell leukemiaT lymphocyte
K-562chronic myelogenous leukemia (CML)bone marrow

Display Conventions and Configuration

This annotation follows the display conventions for composite tracks. The subtracks within this annotation may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For more information about the graphical configuration options, click the Graph configuration help link.

Methods

Chromatin IP was performed as described in Trinklein et al. (2004). Amplified and labeled ChIP DNA was hybridized to oligo tiling arrays produced by NimbleGen, along with a total genomic reference sample. The data for each array were median subtracted (log 2 ratios) and normalized (divided by the standard deviation). The value given for each probe is the transformed mean ratio of ChIP DNA:Total DNA.

Verification

Three biological replicates and two technical replicates were performed. The Myers lab is currently testing the specificity and sensitivity using real-time PCR.

Credits

These data were generated in the Richard M. Myers lab at Stanford University (now at HudsonAlpha Institute for Biotechnology).

References

Trinklein, N.D., Chen, W.C., Kingston, R.E. and Myers, R.M. The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response. Mol. Biol. Cell 15(3), 1254-61 (2004).