Figure 1.

Schematic diagram of the experimental design. For transcriptome analysis of parasite-infected cells, we prepared bradyzoite-infected cells (exposed culture) by inoculating HFF cells with tachyzoites, followed by the induction of bradyzoite differentiation for 6 days in bradyzoite induction medium without CO₂ addition. As a control, HFFs without parasite inoculation were incubated under the same conditions for 6 days (mock-infected treated control). In the exposed culture, the cells were assigned to each category based on the mRNA molecules detected. Parasite-mapped mRNA molecules (parasite load) were used to infer the infection status, and the cells were divided into infected cells and others (cells^{low parasite reads}). Infected cells were further assigned to different subsets based on the presence of the canonical tachyzoite marker SAG1 and bradyzoite marker BAG1 (SAG1+: cells with T. gondii ^{SAG1+/BAG1−}, +/+: cells with both BAG1 and SAG1 markers were detected, BAG1+: cells with T. gondii ^{SAG1−/BAG1+}, ND/ND: cells with T. gondii, but both SAG1 and BAG1 markers were below the detection limit).