|
| Status |
Public on Mar 15, 2011 |
| Title |
NIH3T3_DMSO_18hr_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
NIH3T3, DMSO, 18hr, replicate 1
|
| Organism |
Mus musculus |
| Characteristics |
cell line: NIH3T3
treatment: DMSO
|
| Treatment protocol |
NIH3T3 cells were treated with DMSO, 50 nM rapamycin, or 2 mM PP242 for 18 hours
|
| Growth protocol |
NIH3T3 cells were cultured in DMEM supplemented with 10% BCS and penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using QIAshredder and RNeasy Mini kits (Qiagen). RNA was quantified by Nanodrop and integrity was assessed on an Agilent 2100 Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
RNA was amplified using the whole transcriptome amplification kits (Sigma) following the manufacturer’s protocol, and subsequent Cy3-CTP labeling was performed using one-color labeling kits (NimbleGen). The size distribution and quantity of the amplified product was assessed by Nanodrop and Bioanalyzer.
|
| |
|
| Hybridization protocol |
Equal amounts of Cy3 labeled target were hybridized to Agilent mouse whole genome 4x44K Ink-jet arrays. Hybridizations were performed for 14 hrs, according to the manufacturers protocol.
|
| Scan protocol |
Arrays were scanned using the Agilent microarray scanner.
|
| Description |
Gene expression in NIH3T3 cells after 18hr treatment with DMSO
|
| Data processing |
Raw signal intensities were extracted with Feature Extraction v10.1 software. The dataset was normalized using the quantile normalization method. No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.
|
| |
|
| Submission date |
Mar 07, 2011 |
| Last update date |
Mar 15, 2011 |
| Contact name |
Beatrice Wang |
| E-mail(s) |
beatrice.wang@ucsf.edu
|
| Organization name |
Univeristy of California, San Francisco
|
| Street address |
600 16th Street MC 2280
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE27784 |
Transcriptional profiling of ATP-competitive mTOR inhibitors reveals mTORC1 and mTORC2 specific regulatory networks |
|
