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Sample GSM393167 Query DataSets for GSM393167
Status Public on Jan 05, 2011
Title 40 nM rapamycin, sh p73-1, A
Sample type RNA
 
Source name Rh30 cells, rapamycin, sh p73-1
Organism Homo sapiens
Characteristics cells: Rh30 rhabdomyosarcoma cells
treatment: 40 nM rapamycin
rnai: sh p73-1
Treatment protocol Rh30 cells were infected with lentivirus expressing RNAi targeting p73 or GFP (control) for 3d, then treated with vehicle or 40 nM rapamycin in serum-free media for 24 h.
Growth protocol Cells were cultured in RPMI (Invitrogen) containing 10% Fetal Bovine Serum.
Extracted molecule total RNA
Extraction protocol Total RNA was harvested using the Aurum Total RNA Mini Kit (Bio-Rad) using lysis buffer without beta-Mercaptoethanol.
Label biotin
Label protocol see Vanderbilt Microarray Shared Resource, Affymetrix
 
Hybridization protocol see Vanderbilt Microarray Shared Resource, Affymetrix
Scan protocol see Vanderbilt Microarray Shared Resource, Affymetrix
Description To identify mTOR/p73 target genes, files were imported into GeneSpring GX 9.0.6. The ExonPlier16 summarization algorithm was used, with Core meta probeset level and baseline transformation to the median of all samples. Pairwise comparisons were made between the four categories of samples (Control, sh p73, Rapamycin, Rapamycin + sh p73).
Data processing To identify mTOR/p73 target genes, files were imported into GeneSpring GX 9.0.6. The ExonPlier16 summarization algorithm was used, with Core meta probeset level and baseline transformation to the median of all samples. Pairwise comparisons were made between the four categories of samples (Control, sh p73, Rapamycin, Rapamycin + sh p73).
 
Submission date Apr 16, 2009
Last update date Jan 05, 2011
Contact name Jennifer Pietenpol
Organization name Vanderbilt University Medical Center
Department Biochemistry
Lab 652 PRB
Street address 23rd Ave South at Pierce
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
 
Platform ID GPL6244
Series (2)
GSE15703 Expression data from rapamycin treatment and/or p73 knock-down in Rh30 cells
GSE15719 p73 activity and rapamycin treatment: ChIP-on-Chip and gene expression profiling studies

Data table header descriptions
ID_REF
VALUE ExonPlier16 summarization algorithm in GeneSpring GX, baseline transformation to median of all samples

Data table
ID_REF VALUE
7896736 -0.09205294
7896738 -0.12237215
7896740 -0.14242125
7896742 0.15495682
7896744 0.40759182
7896746 0.0778532
7896748 0.06692219
7896750 0.20896864
7896752 -0.32035637
7896754 0.20856333
7896756 0.046397686
7896759 -0.06521177
7896761 -0.10250044
7896779 1.13E-04
7896798 0.09684324
7896817 0.13799143
7896822 0.06899309
7896859 -0.010702133
7896861 -0.07236433
7896863 0.07176685

Total number of rows: 28869

Table truncated, full table size 556 Kbytes.




Supplementary file Size Download File type/resource
GSM393167.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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