|
| Status |
Public on May 26, 2010 |
| Title |
tc252.normoxia.adherent.1 |
| Sample type |
RNA |
| |
|
| Source name |
Ewing's sarcoma cell line cell line grown under adherent culture condition and under normoxia, replica 1
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: Ewing's sarcoma
cell line: TC-252
genome/variation: EWS-FLI1 fusion type 1
p53 status: wild type
culture conditions: adherent, normoxia
|
| Treatment protocol |
For incubations under normoxia (21% O2), cells were placed in a Thermo-CO2 incubator and grown in a humidified atmosphere containing 5% CO2 (Thermo Electron Corp., Asheville, NC). treatment was applied for 24h.
|
| Growth protocol |
adherent monolayers, maintained in RPMI 1640 (Invitrogen, Germany) supplemented with 10% fetal calf serum (PAA, Pasching, Austria) and 0,01% Penicillin/Streptomycin (PAA, Pasching, Austria). Cells were allowed to recover for 18 h before hypoxia/normoxia treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extrated using the Qiagen RNA extrction kit according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
1.5µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).
|
| |
|
| Hybridization protocol |
Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-A microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
|
| Scan protocol |
Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
|
| Description |
Ewing's sarcoma cell line cell line grown under adherent culture condition and under normoxia
|
| Data processing |
The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the gcRMA algorithm.
|
| |
|
| Submission date |
Nov 25, 2009 |
| Last update date |
May 26, 2010 |
| Contact name |
Maximilian Kauer |
| E-mail(s) |
[email protected]
|
| Organization name |
CCRI, St.Anna Children Cancer Research Institute
|
| Department |
Molecular Biology
|
| Lab |
Heinrich Kovar
|
| Street address |
Zimmermannplatz 10
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE19197 |
Hypoxia modulates EWS-FLI1 transcriptional signature and enhances malignant properties of Ewing’s tumor cells in vitro |
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