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GEO help: Mouse over screen elements for information. |
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| 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
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| 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
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| 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
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| Contributor(s) |
Komashko VM, Acevedo LG, Squazzo SL, Iyengar SS, Rabinovich A, O'Geen H, Green R, Farnham PJ |
| Citation(s) |
18413731, 18347325 |
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| Submission date |
Feb 12, 2008 |
| Last update date |
Jan 18, 2013 |
| Contact name |
Vitalina Komashko |
| E-mail(s) |
vitalina.komashko@sagebase.org
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| Organization name |
Sage Bionetworks
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| Street address |
1100 Fairview Ave N
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platforms (9)
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| 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 |
| GPL4704 |
Nimblegen Human 5K promoter array 1 |
| GPL4865 |
Sentrix MouseRef-8 Expression BeadChip (Target ID) |
| GPL5987 |
Nimblegen Hg18 Promoter (2 of 2) |
| GPL5989 |
Nimblegen Hg18 Promoter (1 of 2) |
| GPL6255 |
Illumina humanRef-8 v2.0 expression beadchip |
| GPL6484 |
NimbleGen Homo sapiens HG18 RefSeq promoter array_386K |
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| Samples (47)
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| GSM262557 |
3T3 G0G1 5-meC |
| GSM262560 |
3T3 Sphase RNAPII |
| GSM262577 |
3T3 Sphase H3me3K27 |
| GSM262582 |
3T3 Sphase H3me3K9 |
| GSM262586 |
3T3 Sphase 5-meC |
| GSM262589 |
Embryoid Bodies RNAPII |
| GSM262590 |
Embryoid Bodies H3me3K27 |
| GSM262690 |
Embryoid Bodies H3me3K9 |
| GSM262694 |
Embryoid Bodies 5-meC |
| GSM262698 |
mESc E14 RNAPII |
| GSM262739 |
mESc E14 H3me3K27 |
| GSM262741 |
mESc E14 H3me3K9 |
| GSM262742 |
mESc E14 5-meC |
| GSM262747 |
MCF7 RNAPII |
| GSM262748 |
MCF7 H3me3K9 |
| GSM262749 |
MCF7 H3me3K27 |
| GSM263125 |
MCF7 5-meC |
| GSM263132 |
Huh7 5-meC |
| GSM263133 |
Primary lung fibroblasts 5-meC |
| GSM263134 |
Primary foot fibroblasts 5-meC |
| GSM263150 |
Primary foreskin fibroblasts 5-meC |
| GSM263588 |
Ntera2 RNAPII promoter 1 |
| GSM263589 |
Ntera2 RNAPII promoter 2 |
| GSM264911 |
mESc E14 RNA expression, technical replicate A |
| GSM264919 |
mESc E14 RNA expression, technical replicate G |
| GSM264923 |
Embryoid Bodies RNA expression, technical replicate C |
| GSM264927 |
Embryoid Bodies RNA expression, technical replicate H |
| GSM264934 |
3T3 G0G1 RNA expression data, technical replicate D |
| GSM264937 |
3T3 G0G1 RNA expression data, technical replicate H |
| GSM264940 |
3T3 Sphase RNA expression, technical replicate E |
| GSM264942 |
3T3 Sphase RNA expression, technical replicate F |
| GSM264969 |
MCF7 RNA expression |
| GSM264974 |
Ntera2 RNA expression |
| GSM264978 |
Huh-7 RNA expression |
| GSM264980 |
Primary foreskin fibroblasts, RNA expression |
| GSM264982 |
Primary lung fibroblasts, RNA expression, technical replicate A |
| GSM264984 |
Primary lung fibroblasts, RNA expression, technical replicate F |
| GSM264985 |
Primary foot fibroblasts, RNA expression, technical replicate B |
| GSM264986 |
Primary foot fibroblasts, RNA expression, technical replicate G |
| GSM265025 |
Normal liver tissue 5-meC, promoter array 1 |
| GSM265035 |
Tumor liver tissue 5-meC, array 1 |
| GSM265404 |
Normal liver tissue 5-meC, promoter array 2 |
| GSM265417 |
Tumor liver tissue 5-meC, array 2 |
| GSM265487 |
Ntera2 5-meC |
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| Relations |
| BioProject |
PRJNA107959 |
| 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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