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Series GSE30984 Query DataSets for GSE30984
Status Public on Jul 27, 2011
Title Genes downstream of p53 mediating its effect on megakaryopoiesis
Organism Homo sapiens
Experiment type Expression profiling by array
Summary In order to examine genes whose expression is altered as a result of the knock-down (KD) of p53, we used gene expression microarray analysis based on the CHRF cell line, a human megakaryoblastic cell line, which upon PMA stimulation undergoes polyploidization, and extends proplatelet-like cytoplasmic protrusions combined with apoptosis. The CHRF cell line has been validated in our laboratory as a good model of in vitro megakaryopoiesis by comparison to hematopoietic stem cells undergoing Mk differentiation. As described, we have previously generated stable p53-KD CHRF cell lines by lentiviral delivery of microRNA-adapted-short hairpin sequences targeting p53 as well as a suitable scrambled-control cell line.
 
Overall design For the microarray analysis we utilized the 4x44K whole human genome microarrays from Agilent. This analysis compared the p53-KD CHRF cells against the control CHRF cells in the absence of PMA treatment and on days 1, 3, 5 and 7 after PMA treatment (5 time-points). p53-KD and control samples were hybridized against each other (direct comparison). We carried out two biological replicate experiments, i.e., 10 measurements of gene expression for each microarray probe. Probes from which >50% of measurements were missing were discarded and not included in the analysis of differential expression. Differentially expressed genes were identified using the significance analysis of microarrays (SAM) with a false discovery rate (FDR) of less than 5%, as implemented in the MultiExperiment Viewer (MeV) tool.
 
Contributor(s) Apostolidis PA, Lindsey S, Miller WM, Papoutsakis ET
Citation(s) 22024107, 22548738
Submission date Jul 27, 2011
Last update date Jan 23, 2019
Contact name Eleftherios Terry Papoutsakis
E-mail(s) papoutsakis@dbi.udel.edu
Organization name University of Delaware
Department Chemical Engineering
Street address 15 Innovation Way
City Newark
State/province DE
ZIP/Postal code 19711
Country USA
 
Platforms (1)
GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)
Samples (31)
GSM767858 p53-KD/Neg-A d0 1st biological rep (Day 0-1 ds1a)
GSM767859 Neg-A/p53-KD d0 1st biological rep (Day 0-1 ds2a)
GSM767860 p53-KD/Neg-A d0 2nd biological rep (Day 0-2 ds1a)
Relations
BioProject PRJNA146195

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
GSE30984_RAW.tar 479.4 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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