Extended Data Fig. 2: Enrichment of C. parvum infected cells and quality control for scRNA-seq.

a, b, Cell populations from a, culture or b, the ileum of an IFN-γ^−/− mouse were sorted to enrich for viable cells infected with fluorescent green C. parvum. Cells sorted from the mouse ileum were also enriched for intestinal epithelial cells based on EPCAM positivity. Sorting gates are outlined in black. The plots were generated with FlowJo 10.8.1. c-e, Violin plots show the distribution of c, genes detected, d, UMIs, and e, percentage of transcripts mapping to rRNA genes across samples after filtering. Filtering cutoffs included a minimum of 100 detected genes and less than 60 percent of transcripts mapping to rRNA. The maximum cutoffs were set per sample according to the pre-processed distribution of detected genes and UMIs. For the in vivo sample, the maximum number of detected genes was 1800 and the maximum number of UMIs was 7500. For timepoints 24, 36, and 42 h, the maximum number of detected genes was 1200 and the maximum number of UMIs was 4000. For timepoints 46 and 54 h, the maximum number of detected genes was 500 and 400 and the maximum number of UMIs was 1000.