|
| Status |
Public on Jan 10, 2011 |
| Title |
HFF-RH+TNF6hr-1 |
| Sample type |
RNA |
| |
|
| Source name |
HFF + RH, 18hr + TNF-alpha, 6hr
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human foreskin fibroblast (HFF)
age: P<22
|
| Treatment protocol |
Parasite strains were syringe lysed, washed at least once with PBS, and added to HFF monolayers for 18-24 hours. Some samples were also stimulated with human TNF for 6 hours.
|
| Growth protocol |
Human foreskin fibroblasts (HFFs) were grown in T25 flasks (BD Biosciences) at 37C, 5% CO2 to confluency. Parasite strains were maintained in vitro by serial passage on monolayers of HFFs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Labeled cDNA were prepared with the NuGEN Applause system from 50-100ng total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 4 ug of cDNA from uninfected samples or 5 ug of cDNA from infected samples were hybridized on GeneChip Human Genome U133A 2.0 Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm. Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. Data was then normalized, setting all data to have a minimum value of 50. Probes called absent or M were also set to have a value of 50.
|
| |
|
| Submission date |
Nov 18, 2010 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Emily E Rosowski |
| E-mail(s) |
rosowski@mit.edu
|
| Organization name |
MIT
|
| Department |
Biology
|
| Lab |
Saeij
|
| Street address |
77 Massachusetts Ave, 68-258d
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE25468 |
Expression data from Human foreskin fibroblasts (HFFs) infected with Toxoplasma gondii. |
| GSE25476 |
Expression data from host cells infected with different strains of Toxoplasma gondii |
|
| Relations |
| Reanalyzed by |
GSE86363 |
