|
| Status |
Public on Aug 02, 2011 |
| Title |
aTC1_d5_dmso_bio rep1 |
| Sample type |
RNA |
| |
|
| Source name |
aTC1 cells, 5-day treatment, DMSO
|
| Organism |
Mus musculus |
| Characteristics |
cell line: aTC1
compound: DMSO
|
| Treatment protocol |
0.5 ul GW8510, dissolved at 1000-fold desired assay concentration (3.3 uM) in DMSO, was added to begin treatment. For 5-day treatment, media was changed and new compound added on day 3. All compound treatments were performed in 0.1% final DMSO concentration. DMSO treatment was used as a vehicle control
|
| Growth protocol |
aTC1 cells were cultured in low-glucose DMEM supplemented by 10% FBS, 10 U/ml penicillin and 50 ug/ml streptomycin. 24 h prior to compound treatment, 200,000 cells were plated per well in a 12-well plate in 500 ul medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following 5-day compound treatment, cells were lysed and RNA isolated using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
500 ng of total RNA was used to prepare complementary RNA (cRNA) target with the Genechip® HT One-Cycle cDNA synthesis Kit (Affymetrix 900687) and the GeneChip® HT IVT Labeling Kit (Affymetrix 900688).
|
| |
|
| Hybridization protocol |
Biotinlyated cRNA targets were normalized, fragmented and hybridized to Affymetrix Mouse 430A 2.0 arrays (GPL8321) using Affymetrix GeneChip® Array Station (GCAS) automation platform.
|
| Scan protocol |
The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332)
|
| Description |
Gene expression data from alpha cells (aTC1) treated with 0.1% DMSO for 5 days, biological replicate 1
|
| Data processing |
The data were analyzed with GenePattern (modules ExpressionFileCreator, PreProcessDataset, and GSEA) using robust multi-array (RMA) analysis for background correction, thresholding and normalization.
|
| |
|
| Submission date |
Aug 01, 2011 |
| Last update date |
Aug 02, 2011 |
| Contact name |
Dina A. Fomina-Yadlin |
| E-mail(s) |
dinafominayadlin@gmail.com
|
| Organization name |
Broad Institute
|
| Street address |
7 Cambridge Center, 3112-D
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL8321 |
| Series (1) |
| GSE31102 |
Expression data from GW8510 treatment of pancreatic cells |
|
