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| Status |
Public on Jun 30, 2009 |
| Title |
Gene expression profiling in p53 and p73 double knockdown HCT116-3(6) cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
The main goal of this study is to integrate gene expression analysis with ChIP-chip study. To examine the relationship between promoter occupancy and gene expression, we transiently depleted p53 and p73 via small interfering RNA (siRNA) in HCT116-3(6) cells and then performed microarray analysis of 32,000 genes before or after HU treatment using the Phalanx expression array platform. We found that only 6%-14% of p53 and p73 bound promoters at FDRMAP <0.05 exhibited significant changes in mRNA expression when p53 and p73 were simultaneously knocked-down by siRNA. The minimal correlation between binding and regulation of expression is consistent with previous observations of the lack of transcriptional effects at many transcription factor binding sites.
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| Overall design |
HCT116-3(6) cells were transiently transfected with lacZ siRNA or p53/p73 siRNA oligo and were then treated with or without HU for 16 hrs. Four biological repeats were performed for each condition (-HU or +HU), with two technical repeats (dye swap) per biological sample.
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| Contributor(s) |
Huang V, Lu X, Jiang Y, Wang JY |
| Citation(s) |
19558638 |
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| Submission date |
Jul 25, 2008 |
| Last update date |
Aug 28, 2014 |
| Contact name |
Vera Huang |
| E-mail(s) |
vera324@yahoo.com
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| Organization name |
UCSD-Moores Cancer Center
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| Department |
Medicine
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| Lab |
Jean Wang Lab
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| Street address |
3855 Health Science Drive, Room 4317
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
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| Samples (16)
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| GSM307286 |
lacZ siRNA transfected HCT116-3(6), replicate 1 |
| GSM307287 |
lacZ siRNA transfected HCT116-3(6), replicate 2 |
| GSM307591 |
lacZ transfected HCT116-3(6), replicate 3 |
| GSM307600 |
lacZ transfected HCT116-3(6), replicate 4 |
| GSM307626 |
lacZ transfected HCT116-3(6), replicate 5 |
| GSM307627 |
lacZ transfected HCT116-3(6), replicate 6 |
| GSM307628 |
lacZ transfected HCT116-3(6), replicate 7 |
| GSM307629 |
lacZ transfected HCT116-3(6), replicate 8 |
| GSM307630 |
p53 and p73 siRNA transfected HCT116-3(6), replicate 1 |
| GSM307631 |
p53 and p73 siRNA transfected HCT116-3(6), replicate 2 |
| GSM307632 |
p53 and p73 siRNA transfected HCT116-3(6), replicate 3 |
| GSM307633 |
p53 and p73 siRNA transfected HCT116-3(6), replicate 4 |
| GSM307634 |
p53 and p73 siRNA transfected HCT116-3(6), replicate 5 |
| GSM307635 |
p53 and p73 siRNA transfected HCT116-3(6), replicate 6 |
| GSM307636 |
p53 and p73 siRNA transfected HCT116-3(6), replicate 7 |
| GSM307637 |
p53 and p73 siRNA transfected HCT116-3(6), replicate 8 |
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| Relations |
| BioProject |
PRJNA113705 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE12242_RAW.tar |
64.9 Mb |
(http)(custom) |
TAR (of GPR) |
| Processed data included within Sample table |
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