Expression profiling of the three clonotypic lineages of Toxoplasma gondii

Expression profiling of the three clonotypic lineages dominating T. gondii populations in North America and Europe provides a first comprehensive view of the parasite transcriptome. Prugniaud, RH, and VEG strain parasites were cultured in human foreskin fibroblast (HFF) cells as previously described (Roos, Donald et al. 1994). Prior to host cell rupture, cells were scraped from the flask and spun at 300g for 9 min. The resultant pellet was lysed with Buffer RLT from the Qiagen RNeasy Mini Kit (Valencia, CA) and RNA was extracted according to the manufacturer’s instructions. Labeled cRNA was created using the One-Cycle Labeling protocol in the Affymetrix GeneChip® IVT Labeling Kit (Santa Clara, CA). Hybridization, washing, and scanning of arrays was performed using standard Affymetrix instrumentation and protocols for 11 micron, 169 format arrays. Biological triplicates were generated for each strain and expression values computed using the RMA implementation (default parameters) in the affy package from Bioconductor (Gentleman, Carey et al. 2004).