|
| Status |
Public on Sep 14, 2009 |
| Title |
Fibroblasts_HealthyControl_5 |
| Sample type |
RNA |
| |
|
| Source name |
Dermal fibroblasts from healthy individual
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Healthy Control
gender: Female
|
| Treatment protocol |
Total RNA was extracted from 1 million cells upon reaching 80% confluence, within passages 2-5 of tissue culture.
|
| Growth protocol |
Fibroblasts were cultured in IMDM (Iscove's Modified Dulbecco's Medium) supplemented with 4 mM L-glutamine, 10% foetal calf serum, 0.1 mg/ml streptomycin, 100U/ml penicylline (Sigma-Aldrich, St. Louis, MO, USA) at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
5 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133A 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G.
|
| Description |
Fibroblasts_HealthyControl_5
|
| 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 |
Jan 08, 2009 |
| Last update date |
Mar 24, 2010 |
| 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 |
GPL571 |
| Series (1) |
| GSE14335 |
Whole genome profiling of fibroblasts from Diamond-Blackfan Anemia patients |
|
