|
| Status |
Public on Jan 05, 2011 |
| Title |
Vehicle control, sh GFP, A |
| Sample type |
RNA |
| |
|
| Source name |
Rh30 cells, vehicle, sh GFP
|
| Organism |
Homo sapiens |
| Characteristics |
cells: Rh30 rhabdomyosarcoma cells
treatment: Vehicle
rnai: sh GFP
|
| 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 |
|
