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Status |
Public on Sep 14, 2009 |
Title |
Fibroblasts_HealthyControl_4 |
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).
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|
|
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_4
|
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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|
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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 |
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