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Status |
Public on Jul 25, 2013 |
Title |
ctrl_rep3 |
Sample type |
RNA |
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Source name |
NSC not irradiated
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Organism |
Mus musculus |
Characteristics |
cell type: Murine ES-derived neural stem cells (NSC)
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Treatment protocol |
10Gy irradiation (Faxitron RX-650 device at 2Gy/min for 5 min)
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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).
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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.
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Scan protocol |
Arrays were scanned using the GeneChip Scanner 3000 7G.
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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.
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Submission date |
May 17, 2012 |
Last update date |
Jul 25, 2013 |
Contact name |
Paola Roncaglia |
Organization name |
SISSA/ISAS (International School for Advanced Studies)
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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 |
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