|
| Status |
Public on Aug 20, 2013 |
| Title |
Toxoplasma gondii RH-JSR 1 |
| Sample type |
RNA |
| |
|
| Source name |
HFF + RH-JSR, 24 hours
|
| Organism |
Toxoplasma gondii |
| Characteristics |
tissue: Human foreskin fibroblast
treatment: infected with RH-JSR for 24 hours
|
| Treatment protocol |
Parasite strains were syringe lysed, washed once with PBS, and added to HFF monolayers for 24 hours.
|
| Growth protocol |
Human foreskin fibroblasts were grown in 6 well plates at 37C, 5% CO2 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, 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 was analyzed with Robust Multi-array Average (RMA), together with Toxoplasma gondii arrays from two other studies (Khan et al, 2009 and Bahl et al, 2010) using default Affymetrix settings in Expression Console version 1.1. The log2 transformed values obtained were then set to minimum of 6.5 or higher.
|
| |
|
| Submission date |
Feb 08, 2013 |
| Last update date |
Aug 20, 2013 |
| Contact name |
Ninghan Yang |
| E-mail(s) |
ynh@mit.edu
|
| Organization name |
MIT
|
| Department |
Biology
|
| Lab |
Saeij
|
| Street address |
77 Massachusetts Ave, 68-270
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL16542 |
| Series (2) |
| GSE44191 |
Parasite gene expression differences between RH-ERP, RH-JSR and GT1 of Toxoplasma gondii. |
| GSE44246 |
Human foreskin fibroblasts (HFFs) infected with type I strains of Toxoplasma gondii |
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