Life cycle of Toxoplasma gondii , and the harvest and hybridization of merozoite mRNA. (A) Life cycle of Toxoplasma gondii . Green circle highlights stages for which microarray expression data exists . Red circle highlights merozoite stage harvested for this study. (B) We obtained intestines from three cats (c48, c50, c52) that had been orally infected 5–6 days previously with the type II parasite TgNmBr1strain in order to isolate merozoite stage parasites. To determine that the purified forms were indeed Toxoplasma, a portion of sample c52 was labeled with mouse α-Me49 (Alexa Fluor 488, yellow). DAPI stained nuclei (blue). (C) mRNAs for two merozoite c52 (Mc52) samples and one for each of the c48 (Mc48) and c50 (Mc50) samples were labeled using the Ambion MessageAmp kit and hybridized to Affymetrix Toxoplasma GeneChips. In order to control for possible strain specific expression we also hybridized two TgNmBr1 tachyzoite mRNA samples (TNm). Data were analyzed in combination with the recently published dataset covering oocyst (Day 0 (OD0), 4 (OD4), 10 (OD10)) to tachyzoite (TD2) to bradyzoite (Day 4 (BD4), 8 (BD8), 21 (BD21)) development in the type II M4 strain . Boxplots of the RMA normalized data show similar distributions and median values across the samples.