|
| Status |
Public on Sep 20, 2009 |
| Title |
WB311, Rapamycin, Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
WB311 cells, 50nM Rapamycin
|
| Organism |
Rattus norvegicus |
| Characteristics |
rapamycin response: Resistant
doubling time: 15.5h
tumorigenic: Yes
|
| Treatment protocol |
10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
|
| Growth protocol |
Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
|
| Scan protocol |
Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
|
| Description |
Spontaneously derived from WB-F344 cell line
|
| Data processing |
The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
|
| |
|
| Submission date |
Aug 14, 2009 |
| Last update date |
Sep 14, 2009 |
| Contact name |
Jennifer Ann Sanders |
| E-mail(s) |
Jennifer_Sanders@brown.edu
|
| Organization name |
Rhode Island Hospital
|
| Department |
Pediatric Endocrinology
|
| Street address |
593 Eddy Street
|
| City |
Providence |
| State/province |
RI |
| ZIP/Postal code |
02903 |
| Country |
USA |
| |
|
| Platform ID |
GPL1355 |
| Series (2) |
| GSE17661 |
Modulation of gene expression by rapamycin in hepatic cell lines, WB-F344 and WB311 |
| GSE17677 |
Modulation of gene expression by rapamycin in hepatic cell lines |
|
