|
| Status |
Public on Sep 09, 2011 |
| Title |
Cells treated with medium as control, biological rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
Cells treated with medium as control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human foreskin fibroblasts (HFF) BJ
|
| Treatment protocol |
Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
|
| Growth protocol |
5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
|
| Description |
Gene expression data from untreated human fibroblast
|
| Data processing |
The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
|
| |
|
| Submission date |
Jun 03, 2009 |
| Last update date |
Sep 09, 2011 |
| Contact name |
Jaime Alfredo Costales |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
Pontificia Universidad Catolica del Ecuador
|
| Department |
Biological Sciences
|
| Lab |
Center for Infectious Disease Research
|
| Street address |
12 de Octubre y Patria
|
| City |
Quito |
| ZIP/Postal code |
NN |
| Country |
Ecuador |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE16416 |
Expression data from human primary fibroblasts treated with Trypanosoma cruzi-conditioned medium |
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