|
| Status |
Public on Oct 01, 2011 |
| Title |
8 dpi in vitro Bradyzoites b |
| Sample type |
RNA |
| |
|
| Source name |
Toxoplasma bradyzoite
|
| Organism |
Toxoplasma gondii |
| Characteristics |
developmental stage: bradyzoite 8 dpi
strain: M4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol (Invitrogen) extraction of total RNA
|
| Label |
biotin
|
| Label protocol |
3’ IVT express kit (Affymetrix ) was used to biotin label 250 ng of total RNA.
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip Hybridization Oven 640, Affymetrix GeneChip Fluidics Station 450
|
| Scan protocol |
Affymetrix GeneChip Scanner 3000 7G
|
| Description |
8 dpi bradyzoites, infected MOI 3 in HFF cells. Grown in RPMI media, no sodium bicarbonate, 1% FCS, 10 mg/ml HEPES, pH 8.0, 37°C without supplemented CO2
|
| Data processing |
Software: Affymetrix Genechip Command Console (AGCC) Data were converted from .cel files and averaged across probes within each probeset using the Bioconductor package affy (version 1.22.1) within the statistical software system R (version 2.10.1), then transformed via a generalized logarithm transformation using the Bioconductor package LMGene (version 2.4.0). Data was transformed via generalized logarithm transformation (glog) and normalized between chips with LOWESS (locally weighted scatterplot smoothing) algorithm using the Bioconductor package LMGene (version 2.4.0, Rocke et al 2010.) A one-way analysis of variance (ANOVA) model was fitted to the data one probeset at a time. For probeset for which the global F test was significant at the 5% level, indicating significant differences between at least two levels of the factor, Tukey HSD post-hoc tests were conducted to test for significant differences among the comparisons of interest.
|
| |
|
| Submission date |
Sep 27, 2011 |
| Last update date |
Jan 24, 2013 |
| Contact name |
Kerry R Buchholz |
| Organization name |
Stanford University
|
| Department |
Microbiology and Immunology
|
| Lab |
John C. Boothroyd Lab
|
| Street address |
Fairchild Bld, 299 Campus Drive D305
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5124 |
| Country |
USA |
| |
|
| Platform ID |
GPL16542 |
| Series (1) |
| GSE32427 |
Transcriptome analysis of oocyst, tachyzoite, and bradyzoite development in the type II Toxoplasma gondii strain M4. |
|
