|
| Status |
Public on Nov 22, 2018 |
| Title |
Short term withdrawal 3T3 2 |
| Sample type |
RNA |
| |
|
| Source name |
Fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
variant: 3T3 SuR/ST-W
treatment: Sunitinib
dose: 5 uM
treatment duration: > 2 months
withdrawal duration: 48 hours
|
| Growth protocol |
Cells were maintained in DMEM supplemented with 5% FBS in the presence or absence of 5μM sunitinib. Growth media was refreshed every 3-4 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from individual samples was extracted using the RNeasy mini kit (QIAGEN; 74104). Genomic DNA was digested using DNase I (QIAGEN; 79254) as described in the on-column DNase digestion protocol from QIAGEN.
|
| Label |
biotin
|
| Label protocol |
Five hundred nanograms total RNA was converted to cDNA, followed by in vitro transcription to generate biotin labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Seven hundred and fifty nanograms of the labeled probes were mixed with hybridization reagents and hybridized overnight at 58oC to the MouseWG-6v2 Expression BeadChip (Illumina; BD-201-0202).
|
| Scan protocol |
After Cy3-streptavidin conjugation the BeadChips were imaged using the Illumina iScan Reader.
|
| Description |
STW.2
SAMPLE 8
|
| Data processing |
The background corrected gene expression levels were extracted from BeadChip using Illumina's Genome Studio (v2011.1) gene expression module (v1.9.0). Gene expression levels were log2 transformed and quantile normalized using lumi in the R-base Bioconductor package.
|
| |
|
| Submission date |
Nov 21, 2018 |
| Last update date |
Nov 22, 2018 |
| Contact name |
John M.L. Ebos |
| E-mail(s) |
John.Ebos@RoswellPark.org
|
| Organization name |
Roswell Park Cancer Institute
|
| Department |
Department of Cancer Genetics and Genomics
|
| Street address |
Elm & Carlton Streets
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
| |
|
| Platform ID |
GPL18752 |
| Series (1) |
| GSE122820 |
Gene expression changes in mouse fibroblasts (3T3) after sunitinib resistance and acute and chronic withdrawal |
|
