|
| Status |
Public on May 22, 2008 |
| Title |
Strain CL16 Tachyzoite |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
Tachyzoites
|
| Organism |
Toxoplasma gondii |
| Characteristics |
24 h in vitro tachyzoite
|
| Treatment protocol |
None
|
| Growth protocol |
Tachyzoites were grown in human foreskin fibroblasts in the presence of 10% serum in DMEM. Cells were infected at an MOI of 10 tachyzoites per cell and growth was carried out for 24h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol using the manufacturers instruction. mRNA was isolated from total RNA using the oligotex mRNA isolation kit (Qiagen)
|
| Label |
Cy5
|
| Label protocol |
cDNA was synthesized from mRNA using oligo-dT priming and reverse transcription. cDNA was then labeled with Cy5-dUTP using klenow (exo minus) and random primers
|
| |
|
| Channel 2 |
| Source name |
empty pBluescript vector, in vitro transcribed
|
| Organism |
synthetic construct |
| Characteristics |
common reference (in vitro transcribed RNA)
|
| Treatment protocol |
None
|
| Growth protocol |
Vector was propagated in DH5alpha cells.
|
| Extracted molecule |
other |
| Extraction protocol |
Plasmid was isolated using Qiagen miniprep kit.
|
| Label |
Cy3
|
| Label protocol |
The polylinker region of the isolated plasmid was PCR-amplified using T3 and T7 primers. The PCR product was gel-purified using a Qiagen gel purification kit, and used as a template for in vitro transcription. The polylinker was transcribed in the presence of dUTP using the T7 RNA polymerase transcription kit (Maxiscript; Ambion).
|
| |
|
| |
| Hybridization protocol |
Labeled cDNA was applied to array slides, covered with a coverslip, and hybridized at 68 degrees for 16-20 h. Slide were washed sequentially in 2X SSC, 1X SSC, and 0.5X SSC for 5 min each.
|
| Scan protocol |
Slides were scanned on a GenePix scanner
|
| Description |
PDS X CTG F1 Progeny clone CL16
|
| Data processing |
log2 ratios were normalized to a mean of 0 for all slides
|
| |
|
| Submission date |
May 14, 2008 |
| Last update date |
May 20, 2008 |
| Contact name |
Jon Boyle |
| E-mail(s) |
boylej@stanford.edu
|
| Organization name |
Stanford University School of Medicine
|
| Department |
Microbiology and Immunology
|
| Lab |
Boothroyd Lab
|
| Street address |
299 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
92305 |
| Country |
USA |
| |
|
| Platform ID |
GPL6851 |
| Series (2) |
| GSE11437 |
Expression QTL mapping of Toxoplasma gondii genes, Bradyzoite array |
| GSE11515 |
Expression QTL mapping of Toxoplasma gondii genes |
|
