|
| Status |
Public on Jul 27, 2010 |
| Title |
7K B, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Mutant 7K, bradyzoites
|
| Organism |
Toxoplasma gondii |
| Characteristics |
strain: RH strain
|
| Growth protocol |
T. gondii tachyzoites were maintained by serial passage in primary cultures of Human foreskin fibroblast (HFF) cells. Parasites were induced to differentiate into bradyzoites in low [CO2], resulting in pyrimidine starvation. CO2 depletion was accomplished by inoculating tachyzoites in host cells in minimal essential medium without NaHCO3 but containing 25 mM HEPES.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Qiagen kit according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
RNA amplification, fragmentation, and labeling were performed using the Ovation V2 and Encore reagents by NuGEN technologies.
|
| |
|
| Hybridization protocol |
GeneChip hybridization mixes were prepared using 4ug of the biotin-labeled fragmented cDNA and hybridized to the ToxoGeneChip array as per manufacturer’s recommendations for 16 hr at 45C at 60 rpm, double stained with streptavidin-PE using the Affymetrix 450 fluidics station.
|
| Scan protocol |
GeneChips were scanned with the Affymetrix 3000-G7 scanner.
|
| Description |
OWP-B-D-matrajt-070607-tox.CEL
|
| Data processing |
Raw GeneChip data includes a collection of images, one for each probe and chip. Each image is summarized by Affymetrix GCOS software using one probe intensity (in CEL files, one per chip). We calculated a summary measure of expression, for each probe set, using the Robust Multichip Average (RMA) method using R and BioConductor tools (aroma.affymetrix package of Bengtesson).
|
| |
|
| Submission date |
Jul 26, 2010 |
| Last update date |
Jan 24, 2013 |
| Contact name |
Mariana Matrajt |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Vermont
|
| Street address |
95 Carrigan Drive
|
| City |
Burlington |
| ZIP/Postal code |
05405 |
| Country |
USA |
| |
|
| Platform ID |
GPL16542 |
| Series (1) |
| GSE23174 |
Expression data from Toxoplasma gondii mutants and wild-type during bradyzoite differentiation in vitro |
|
