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Series GSE12242 Query DataSets for GSE12242
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
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.
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.
Contributor(s) Huang V, Lu X, Jiang Y, Wang JY
Citation(s) 19558638
Submission date Jul 25, 2008
Last update date Aug 28, 2014
Contact name Vera Huang
Organization name UCSD-Moores Cancer Center
Department Medicine
Lab Jean Wang Lab
Street address 3855 Health Science Drive, Room 4317
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (1)
GPL6254 Phalanx Human OneArray
Samples (16)
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
BioProject PRJNA113705

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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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