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Series GSE10504 Query DataSets for GSE10504
Status Public on Mar 31, 2008
Title Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by genome tiling array
Methylation profiling by array
Summary We compared 12 different cell populations, including embryonic stem cells before and during differentiation into embryoid bodies as well as various types of normal and tumor cells to determine if pluripotent vs. differentiated cell types use different mechanisms to establish their transcriptome. We first identified genes that were not expressed in the 12 different cell populations and then determined which of them were regulated by histone methylation, DNA methylation, at the step of productive elongation, or by the inability to establish a pre-initiation complex. For these experiments, we performed chromatin immunoprecipitation using antibodies to H3me3K27, H3me3K9, 5-methyl cytosine, and POLR2A. We found that a) the percentage of low expressed genes bound by POLR2A, H3me3K27, H3me3K9, or 5-methyl-cytosine is similar in all 12 cell types, regardless of differentiation or neoplastic state; b) a gene is generally repressed by only one mechanism; and c) distinct classes of genes are repressed by certain mechanisms. We further characterized two transitioning cell populations, 3T3 cells progressing from G0/G1 into S phase and mES cells differentiating into embryoid bodies. We found that the transient regulation through the cell cycle was achieved predominantly by changes in the recruitment of the general transcriptional machinery or by post-POLR2A recruitment mechanisms. In contrast, changes in chromatin silencing were critical for the permanent changes in gene expression in cells undergoing differentiation.
Keywords: ChIP-chip, RNA expression
Overall design 48 ChIP-chip arrays; 12 expression arrays (6 of them in duplicates).
47 samples are included in this series, the rest can be found in supplementary info to the following papers: O'Geen 2007, Acevedo 2008, Acevedo 2007, Rinn 2007
Contributor(s) Komashko VM, Acevedo LG, Squazzo SL, Iyengar SS, Rabinovich A, O'Geen H, Green R, Farnham PJ
Citation(s) 18413731, 18347325
Submission date Feb 12, 2008
Last update date Jan 18, 2013
Contact name Vitalina Komashko
Organization name Sage Bionetworks
Street address 1100 Fairview Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
Platforms (9)
GPL3787 Nimblegen Human 1.5 kb promoter
GPL3793 Nimblegen Mouse 1.5 kb promoter array [2006-11-16_MM5_min_promoter]
GPL3930 Nimblegen human 5K promoter array 2
Samples (47)
GSM258039 3T3 G0G1 RNAPII
GSM262288 3T3 G0G1 H3me3K27
GSM262289 3T3 G0G1 H3me3K9
BioProject PRJNA107959

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE10504_RAW.tar 739.9 Mb (http)(custom) TAR (of CSV, IDAT, JPG, PAIR, TIFF, TXT, XML)
Processed data included within Sample table

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