|
| Status |
Public on Jul 25, 2013 |
| Title |
ctrl_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
NSC not irradiated
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Murine ES-derived neural stem cells (NSC)
|
| Treatment protocol |
10Gy irradiation (Faxitron RX-650 device at 2Gy/min for 5 min)
|
| Growth protocol |
Euromed-N cell culture medium (Euroclone), supplemented with L-Gln and P/S, 1x N2 supplement (Invitrogen), 20ng/ml each murine EGF and FGF2 at 5% CO2 and 37° C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction, Qiagen RNA mini column purification, isopropanol precipitation.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
cRNA was hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Arrays were scanned using the GeneChip Scanner 3000 7G.
|
| Data processing |
Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment using packages from BioConductor. Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Probes with low intensity values (less than 100) in all arrays were also excluded from statistical analysis.
|
| |
|
| Submission date |
May 17, 2012 |
| Last update date |
Jul 25, 2013 |
| Contact name |
Paola Roncaglia |
| Organization name |
SISSA/ISAS (International School for Advanced Studies)
|
| Department |
Neurobiology
|
| Street address |
via Bonomea 265
|
| City |
Trieste |
| State/province |
TS |
| ZIP/Postal code |
34136 |
| Country |
Italy |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE38031 |
DNA damage-induced differentiation of NSC |
|
