Supplementary tables described below.

Table A: Summary of average total RNASeq reads mapped. Table B: Numbers of raw reads mapped to rat genes or exons from CLC Genomics. Table C: Numbers of raw reads mapped to Toxoplasma genes or exons from CLC Genomics. Table D: Final list of 16416 rat genes with average exon reads included in analysis pipeline with RPKM values and fold changes. Only genes with ≥ 5 exon reads are included. Table E: Final list of 6469 Toxoplasma genes with average adjusted exon reads that were included in analysis pipeline with RPKM values and fold-changes. Only genes with ≥ 5 exon reads are included. Table F: Results of SAMseq statistical analyses for all pairwise comparisons performed. Table G: Rat genes with increased expression during infection with tachyzoites. Ranked by ratio of read numbers for TZ/Mock. Table H: Toxoplasma genes with higher expression in intracellular sporozoites compared to tachyzoites. Ranked by ratio of read numbers for SPZ/TZ; inf = infinity; Only genes with ≥ 5 exon reads are included. Table I: Toxoplasma genes with higher expression in intracellular tachyzoites compared to sporozoites. Only genes with at least 20 reads in TZ are included in the table. Ranked by ratio of read numbers for TZ/SPZ; inf = infinity. Table J: Significantly higher genes encoding hypothetical proteins with predicted signal peptides in SPZ vs. TZ. Ranked by ratio of read numbers for SPZ/TZ; inf = infinity.
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