|
| Status |
Public on Aug 01, 2015 |
| Title |
HFF-untreat,RH,IFNY |
| Sample type |
RNA |
| |
|
| Source name |
HFF, untreated, RH infected 1hr, IFNgamma treated 1hr
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human foreskin fibroblasts
parasite strain: RH 1-1
treated: no
infection: yes
stimulated: yes
|
| Treatment protocol |
HFFs were pre-treated (or not) with 50ug/ml CHX for 40min. Parasites were syringe lysed, washed at least once with PBS, and added to HFFs (still in the presence of CHX) for one hours. Media was replaced (+/- CHX) on uninfected cell samples. Cells were then stimulated with 100U/ml human IFN-γ for one hour (still in the presence of CHX). Media was replaced (+/- CHX) on unstimulated cell samples. CHX treatment inhibited IFN-γ induced protein expression without causing the cells to appear sick.
|
| Growth protocol |
1.5-2x105 HFFs were grown in 12-well plates (BD Biosciences) at 37C, 5% CO2. An RH 1-1 type I parasite strain was 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, 5 ug of cDNA from samples were hybridized on GeneChip Mouse Genome 430A 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.
|
| |
|
| Submission date |
Jan 06, 2012 |
| Last update date |
Aug 01, 2015 |
| 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 |
GPL571 |
| Series (1) |
| GSE34916 |
Expression data from cyclohexamide treated Human Foreskin Fibroblasts (HFFs) infected with type I Toxoplasma gondii and stimulated with interferon gamma. |
|
