|
| Status |
Public on Feb 25, 2010 |
| Title |
RCC-MF_caffeine_2 (GINI) |
| Sample type |
RNA |
| |
|
| Source name |
cell line derived from clear cell renal cell carcinoma tumor
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RCC-MF (KTCTL-1M )
depositor: Cell Lines Service, www.cellbank.de
gender: Male
sample type: clear cell renal cell carcinoma (lung metastasis)
tumor stage: pT2,N1,Mx/GII-III (lung-metastasis)
age of diagnosis: 63
treatment: Caffeine
|
| Treatment protocol |
Cells were grown to approximately 70 % confluence in 75 cm flasks, medium was refreshed, caffeine was added (10 mM).Following 8 hrs of incubation (37 °C, 5% CO2), cells were trypsinized and harvested
|
| Growth protocol |
The cell lines were maintained in RPMI 1640 (Sigma) supplemented with 10 % fetal calf serum (Gibco), penicillin (1.0 U/l) (Gibco), streptomycin (1 μg/ul) (Gibco), glutamin (2.0 mM) (Gibco). Cells were grown in an incubator at 37˚C, 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNEasy miniKIT (Qiagen) following the manufacturer's protocol
|
| Label |
biotin
|
| Label protocol |
Total RNA was labeled using the Illumina ® TotalPrep™-96 RNA amplification kit following the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Transcript abundance in treated and untreated cells was measured using Human HT-12_V3_Beadchips (48K) (Ilumina)following the manufacturer's protocol
|
| Scan protocol |
Arrays were scanned using an Illumina scanner
|
| Description |
n/a
|
| Data processing |
Microarray data normalization was performed using the Lumi package implemented in R. Data were transformed and normalized using variance-stabilizing transformation followed by robust spline normalization.
|
| |
|
| Submission date |
Feb 23, 2010 |
| Last update date |
Feb 24, 2010 |
| Contact name |
Gerben Duns |
| E-mail(s) |
g.duns@medgen.umcg.nl
|
| Organization name |
Genetics Department, Groningen University
|
| Street address |
Oostersingel, ingang 47, 2nd floor, room E2.036
|
| City |
Groningen |
| ZIP/Postal code |
9700 RB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6947 |
| Series (1) |
| GSE20491 |
Identification of transcripts harboring premature termination codons by NMD inhibition in a panel of CCRCC cell lines |
|
