There are two experiments included in this particular GEO accession: For the first, freshly excysted sporozoites of T. gondii VEG or H. hammondi Amer1 were put into culture for 2 days, and then either allowed to continue growth in control (pH 7.2, 5% C02, 10% FCS) or high pH, bradyzoite-inducing (pH 8.2, low C02, 1% FCS) conditions for 3 days and then harvested for RNAseq analysis. In the second, T. gondii strain VEG was genetically manipulated to ablate either the ROCY1 gene (TGVEG_311100) or the BFD1 gene (TGME49_200385) and then compared to Wild Type VEG in a bradyzoite induction assay. Specifically, each parasite line was grown for 2 days in control conditions (same as above) or bradyzoite induction conditions (same as above) and then harvested for RNAseq. Data were mapped to the parasite genomes transcript abundance was normalized and calculated using DESeq2. Overall design: For the first experiment each condition has three biological replicates, where each biological replicate was a distinct well of a 24 well plate. For the second experiment each condition has between 2 and 3 biological replicates, where each biological replicate is a separate well of a 24 well plate.