|
| Status |
Public on Dec 06, 2013 |
| Title |
WM_K2 |
| Sample type |
RNA |
| |
|
| Source name |
control WM793B cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: WM793B human melanoma cell line
cell line: ATCC, CRL-2813
|
| Treatment protocol |
Hypoxic conditions were introduced by incubating the cells in 1% oxygen using oxygen flow-regulated incubator for 72 h (chronic hypoxia) or for 4/12 hour periods of 1% oxygen interchanged with periods of 21% oxygen (cycling hypoxia). Control cells were cultured in standard conditions (21% oxygen) for 72 h.
|
| Growth protocol |
The human cancer cells were grown in CO2 incubator at 37°C in the following culture media: PC-3 - RPMI (Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS; Gibco BRL), SK-OV-3 - McCoy’s medium (Sigma-Aldrich) supplemented with 10% FBS (Gibco BRL), WM793B - 2% Tu medium (Sigma-Aldrich) supplemented with 2% FBS (Gibco BRL), bovine insulin (0.005 mg/ml) and 1.68 mmol/l CaCl2 (Sigma-Aldrich).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Total RNA (5 μg) was used for synthesis of double stranded cDNA according to manufacturer's instructions. Half of the cDNA volume was used for synthesis of biotynylated cRNA with reagents recommended by Affymetrix.
|
| |
|
| Hybridization protocol |
Following fragmentation, 16 μg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
Arrays were scanned by GeneChip Scanner 3000 and the data was acquired using GCOS 1.2 software (Affymetrix).
|
| Description |
WM793B melanoma cells cultured in control conditions (21% oxygen), biological replica 2
|
| Data processing |
The CEL files were pre-processed using the GC-RMA algorithm available in R environment as the Bioconductor gcrma package.
|
| |
|
| Submission date |
Dec 05, 2013 |
| Last update date |
Dec 06, 2013 |
| Contact name |
Magdalena Olbryt |
| E-mail(s) |
[email protected]
|
| Organization name |
Cancer Center and Institute of Oncology
|
| Department |
Center for Translational Research and Molecular Biology of Cancer
|
| Street address |
Wybrzerze AK 15
|
| City |
Gliwice |
| ZIP/Postal code |
44-100 |
| Country |
Poland |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE53012 |
Expression data from three human cancer cell lines (PC-3, SK-OV-3, WM793B) exposed to experimental cycling and chronic hypoxa in vitro |
|
